--- ncbi-tools6-6.1.20070822.orig/api/txalign.c +++ ncbi-tools6-6.1.20070822/api/txalign.c @@ -6291,7 +6291,7 @@ if(seq_int1 != NULL) { /* This line should be checked for correctness */ - if((line1[line_index] = BSGetByte(b_store)) == EOF) + if((line1[line_index] = BSGetByte(b_store)) == (Char)EOF) line1[line_index] = '?'; if(dna_strand != Seq_strand_minus) --- ncbi-tools6-6.1.20070822.orig/api/aliread.c +++ ncbi-tools6-6.1.20070822/api/aliread.c @@ -383,7 +383,7 @@ Int4 segmentLen = 0; Int4 segmentCount = 1; Boolean done = FALSE; - Char ch = 0; + Int2 ch = 0; /* Allocate memory for the line. More */ /* can be added later as necessary. */ @@ -402,12 +402,12 @@ /* Process the current character */ - ch = (Char) NLM_GETC (alignFilePtr); + ch = NLM_GETC (alignFilePtr); if (ch == '\n') { done = TRUE; - ch = (Char) NLM_GETC (alignFilePtr); + ch = NLM_GETC (alignFilePtr); if (ch != '\r') { ungetc (ch, alignFilePtr); --- ncbi-tools6-6.1.20070822.orig/doc/man/nps2gps.1 +++ ncbi-tools6-6.1.20070822/doc/man/nps2gps.1 @@ -1,16 +1,17 @@ -.TH NPS2GPS 1 2005-11-04 NCBI "NCBI Tools User's Manual" +.TH NPS2GPS 1 2007-09-08 NCBI "NCBI Tools User's Manual" .SH NAME nps2gps \- convert nucleotide-protein sets to ASN.1 genomic product sets .SH SYNOPSIS .B nps2gps [\|\fB\-\fP\|] +[\|\fB\-F\fP\|] [\|\fB\-L\fP\|] [\|\fB\-R\fP\|] [\|\fB\-f\fP\ \fIstr\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-o\fP\ \fIfilename\fP\|] -[\|\fB\-p\fP\ \fIstr\fP\|] -[\|\fB\-r\fP\ \fIstr\fP\|] +[\|\fB\-p\fP\ \fIpath\fP\|] +[\|\fB\-r\fP\ \fIpath\fP\|] [\|\fB\-x\fP\ \fIstr\fP\|] .SH DESCRIPTION \fBnps2gps\fP converts NCBI Bioseq-sets from simple nucleotide-protein @@ -22,6 +23,9 @@ \fB\-\fP Print usage message .TP +\fB\-F\fP +Map by Feature ID +.TP \fB\-L\fP Lock components in advance .TP @@ -37,10 +41,10 @@ \fB\-o\fP\ \fIfilename\fP Single output file (default = stdout) .TP -\fB\-p\fP\ \fIstr\fP +\fB\-p\fP\ \fIpath\fP Path to files for batch conversion .TP -\fB\-r\fP\ \fIstr\fP +\fB\-r\fP\ \fIpath\fP Path for results of batch conversion .TP \fB\-x\fP\ \fIstr\fP --- ncbi-tools6-6.1.20070822.orig/doc/man/tbl2asn.1 +++ ncbi-tools6-6.1.20070822/doc/man/tbl2asn.1 @@ -1,4 +1,4 @@ -.TH TBL2ASN 1 2006-05-29 NCBI "NCBI Tools User's Manual" +.TH TBL2ASN 1 2007-09-08 NCBI "NCBI Tools User's Manual" .SH NAME tbl2asn \- prepare a GenBank submission using an ASCII feature table .SH SYNOPSIS @@ -6,18 +6,22 @@ [\|\fB\-\fP\|] [\|\fB\-B\fP\ \fIstr\fP\|] [\|\fB\-C\fP\ \fIstr\fP\|] +[\|\fB\-D\fP\ \fIfilename\fP\|] [\|\fB\-E\fP\ \fIstr\fP\|] -[\|\fB\-F\fP\|] +[\|\fB\-F\fP\ \fIstr\fP|] [\|\fB\-G\fP\ \fIstr\fP\|] [\|\fB\-H\fP\|] +[\|\fB\-K\fP\|] [\|\fB\-L\fP\|] [\|\fB\-M\fP\ \fIstr\fP\|] +[\|\fB\-O\fP\|] [\|\fB\-P\fP\|] [\|\fB\-Q\fP\|] [\|\fB\-R\fP\|] [\|\fB\-S\fP\|] [\|\fB\-T\fP\|] [\|\fB\-U\fP\|] +[\|\fB\-W\fP\|] [\|\fB\-X\fP\ \fIstr\fP\|] [\|\fB\-Y\fP\ \fIfilename\fP\|] [\|\fB\-a\fP\ \fIstr\fP\|] @@ -25,6 +29,7 @@ [\|\fB\-c\fP\|] [\|\fB\-d\fP\|] [\|\fB\-e\fP\|] +[\|\fB\-f\fP\ \fIfilename\fP\|] [\|\fB\-g\fP\|] [\|\fB\-h\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] @@ -64,11 +69,14 @@ \fB\-C\fP\ \fIstr\fP Genome Center tag .TP +\fB\-D\fP\ \fIfilename\fP +Descriptors file +.TP \fB\-E\fP\ \fIstr\fP Alignment End gap characters .TP \fB\-F\fP -Feature ID links +Feature ID links (\fBo\fP by Overlap, \fBp\fP by Product) .TP \fB\-G\fP\ \fIstr\fP Alignment middle Gap characters @@ -76,12 +84,18 @@ \fB\-H\fP Implicit gaps .TP +\fB\-K\fP +Safe Bioseq-set +.TP \fB\-L\fP Force Local protein_id/transcript_id .TP \fB\-M\fP\ \fIstr\fP Alignment Match characters .TP +\fB\-O\fP +Allow run-on ORFs +.TP \fB\-P\fP Alignment is Proteins .TP @@ -100,6 +114,9 @@ \fB\-U\fP Remove Unnecessary gene xref .TP +\fB\-W\fP +Log progress +.TP \fB\-X\fP\ \fIstr\fP Alignment missing characters .TP @@ -121,6 +138,9 @@ \fB\-e\fP Read PHRAP/ACE format .TP +\fB\-f\fP\ \fIfilename\fP +Single table file +.TP \fB\-g\fP Input is a genomic product set .TP --- ncbi-tools6-6.1.20070822.orig/doc/man/blast2.1 +++ ncbi-tools6-6.1.20070822/doc/man/blast2.1 @@ -0,0 +1 @@ +.so man1/blast.1 --- ncbi-tools6-6.1.20070822.orig/doc/man/Nentrez.1 +++ ncbi-tools6-6.1.20070822/doc/man/Nentrez.1 @@ -1,4 +1,4 @@ -.TH NENTREZ 1 2001-11-21 NCBI "NCBI Tools User's Manual" +.TH NENTREZ 1 2007-09-08 NCBI "NCBI Tools User's Manual" .SH NAME Nentrez \- a graphical client for the NCBI Entrez retrieval system .SH SYNOPSIS @@ -15,5 +15,4 @@ .SH SEE ALSO .ad l .BR entrez2 (1), -.BR netentcf (1), --- ncbi-tools6-6.1.20070822.orig/doc/man/formatdb.1 +++ ncbi-tools6-6.1.20070822/doc/man/formatdb.1 @@ -1,4 +1,4 @@ -.TH FORMATDB 1 2005-11-04 NCBI "NCBI Tools User's Manual" +.TH FORMATDB 1 2006-10-20 NCBI "NCBI Tools User's Manual" .SH NAME formatdb \- format protein or nucleotide databases for BLAST .SH SYNOPSIS @@ -99,9 +99,9 @@ .TP \fB\-v\fP\ \fIN\fP Break up large FASTA files into 'volumes' of size \fIN\fP million -letters. As part of the creation of a volume, \fBformatdb\fP writes a -new type of BLAST database file, called an alias file, with the -extension 'nal' or 'pal'. +letters (4000 by default). As part of the creation of a volume, +\fBformatdb\fP writes a new type of BLAST database file, called an +alias file, with the extension 'nal' or 'pal'. .SH AUTHOR The National Center for Biotechnology Information. .SH SEE ALSO --- ncbi-tools6-6.1.20070822.orig/doc/man/cleanasn.1 +++ ncbi-tools6-6.1.20070822/doc/man/cleanasn.1 @@ -1,54 +1,59 @@ -.TH CLEANASN 1 2006-05-29 NCBI "NCBI Tools User's Manual" +.TH CLEANASN 1 2006-10-20 NCBI "NCBI Tools User's Manual" .SH NAME -cleanasn \- clean up irregularities in NCBI ASN.1 Seq-entry objects +cleanasn \- clean up irregularities in NCBI ASN.1 objects .SH SYNOPSIS .B cleanasn [\|\fB\-\fP\|] +[\|\fB\-F\fP\ \fIstr\fP\|] +[\|\fB\-K\fP\ \fIstr\fP\|] +[\|\fB\-N\fP\ \fIstr\fP\|] [\|\fB\-R\fP\|] -[\|\fB\-c\fP\ \fIstr\fP\|] +[\|\fB\-T\fP\|] +[\|\fB\-a\fP\ \fIstr\fP\|] +[\|\fB\-b\fP\|] +[\|\fB\-c\fP\|] [\|\fB\-f\fP\ \fIstr\fP\|] -[\|\fB\-l\fP\ \fIstr\fP\|] -\fB\-p\fP\ \fIpath\fP +[\|\fB\-i\fP\ \fIfilename\fP\|] +[\|\fB\-l\fP\ \fIfilename\fP\|] +[\|\fB\-o\fP\ \fIfilename\fP\|] +[\|\fB\-p\fP\ \fIpath\fP\|] [\|\fB\-r\fP\ \fIpath\fP\|] -[\|\fB\-t\fP\|] +[\|\fB\-x\fP\ \fIext\fP\|] .SH DESCRIPTION \fBcleanasn\fP is a utility program to clean up irregularities in NCBI -ASN.1 Seq-entry or Seq-submit objects. +ASN.1 objects. .SH OPTIONS A summary of options is included below. .TP \fB\-\fP Print usage message .TP -\fB\-R\fP -Enable remote fetching from NCBI's ID database -.TP -\fB\-c\fP\ \fIstr\fP -Perform general clean-ups, per the flags in \fIstr\fP: +\fB\-F\fP\ \fIstr\fP +Clean up features, per the flags in str: .RS .PD 0 -.IP b -BasicSeqEntryCleanup -.IP s -SeriousSeqEntryCleanup +.IP u +Remove User-objects +.IP d +Remove db_xrefs +.IP r +Remove redundant gene xrefs .PD .RE .TP -\fB\-f\fP\ \fIstr\fP -Remove extraneous features, per the flags in \fIstr\fP: +\fB\-K\fP\ \fIstr\fP +Perform a general cleanup, per the flags in str: .RS .PD 0 -.IP u -Remove User objects -.IP d -Remove Database cross-references -.IP r -Remove Redundant gene cross-references +.IP b +BasicSeqEntryCleanup +.IP s +SeriousSeqEntryCleanup .PD .RE .TP -\fB\-l\fP\ \fIstr\fP -Link related features, per the flags in \fIstr\fP: +\fB\-N\fP\ \fIstr\fP +Clean up links, per the flags in str: .RS .PD 0 .IP o @@ -57,16 +62,64 @@ LinkCDSmRNAbyProduct .IP r ReassignFeatureIDs +.IP c +ClearFeatureIDs .PD .RE .TP +\fB\-R\fP +Remote fetching from ID (NCBI sequence databases) +.TP +\fB\-T\fP +Taxonomy Lookup +.TP +\fB\-a\fP\ \fIstr\fP +ASN.1 type +.RS +.PD 0 +.IP a +Any (default) +.IP e +Seq-entry +.IP b +Bioseq +.IP s +Bioseq-set +.IP m +Seq-submit +.IP t +Batch Processing [String] +.PD +.RE +.TP +\fB\-b\fP +Input ASN.1 is Binary +.TP +\fB\-c\fP +Input ASN.1 is Compressed +.TP +\fB\-f\fP\ \fIstr\fP +Substring filter +.TP +\fB\-i\fP\ \fIfilename\fP +Single input file (defaults to stdin) +.TP +\fB\-l\fP\ \fIfilename\fP +Log file +.TP +\fB\-o\fP\ \fIfilename\fP +Single output file (defaults to stdout) +.TP \fB\-p\fP\ \fIpath\fP -Path to input files +Process all matching files in \fIpath\fP .TP \fB\-r\fP\ \fIpath\fP -Path for Results (changes are otherwise made in place) +Path for results .TP -\fB\-t\fP -Enable Taxonomy lookup +\fB\-x\fP\ \fIext\fP +File selection suffix for use with \fB\-p\fP (defaults to \fB.ent\fP) .SH AUTHOR The National Center for Biotechnology Information. +.SH SEE ALSO +asnval (1), +sequin (1). --- ncbi-tools6-6.1.20070822.orig/doc/man/entrez2.1 +++ ncbi-tools6-6.1.20070822/doc/man/entrez2.1 @@ -1,4 +1,4 @@ -.TH ENTREZ2 1 2001-11-21 NCBI "NCBI Tools User's Manual" +.TH ENTREZ2 1 2007-10-07 NCBI "NCBI Tools User's Manual" .SH NAME entrez2 \- a graphical client for the NCBI Entrez retrieval system .SH SYNOPSIS @@ -14,6 +14,4 @@ The National Center for Biotechnology Information. .SH SEE ALSO .ad l -.BR Nentrez (1), -.BR netentcf (1), --- ncbi-tools6-6.1.20070822.orig/doc/man/asn2gb.1 +++ ncbi-tools6-6.1.20070822/doc/man/asn2gb.1 @@ -1,4 +1,4 @@ -.TH ASN2GB 1 2006-05-29 NCBI "NCBI Tools User's Manual" +.TH ASN2GB 1 2006-10-20 NCBI "NCBI Tools User's Manual" .SH NAME asn2gb \- convert ASN.1 biological data to a GenBank-style flat format .SH SYNOPSIS @@ -206,10 +206,14 @@ Custom flags (all default to off): .RS .PD 0 -.IP 2 -Hide most imported features .IP 4 -Hide SNP features +Hide features +.IP 1792 +Hide references +.IP 8192 +Hide sources +.IP 262144 +Hide translations .PD .RE .\" .TP @@ -227,4 +231,5 @@ .BR asn2fsa (1), .BR asn2xml (1), .BR asndhuff (1), -.BR insdseqget (1). +.BR insdseqget (1), +asn2gb.txt. --- ncbi-tools6-6.1.20070822.orig/doc/man/blast.1 +++ ncbi-tools6-6.1.20070822/doc/man/blast.1 @@ -1,6 +1,6 @@ -.TH BLAST 1 2006-05-29 NCBI "NCBI Tools User's Manual" +.TH BLAST 1 2007-09-11 NCBI "NCBI Tools User's Manual" .SH NAME -bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop \- Basic Local Alignment Search Tool +bl2seq, blast2, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop \- Basic Local Alignment Search Tool .SH SYNOPSIS .B bl2seq [\|\fB\-\fP\|] @@ -32,7 +32,7 @@ [\|\fB\-r\fP\ \fIN\fP\|] [\|\fB\-t\fP\ \fIN\fP\|] .PP -.B blast +.B blast2 [\|\fB\-\fP\|] [\|\fB\-B\fP\ \fIN\fP\|] [\|\fB\-D\fP\ \fIN\fP\|] @@ -61,8 +61,8 @@ [\|\fB\-c\fP\|] [\|\fB\-d\fP\ \fIstr\fP\|] [\|\fB\-e\fP\ \fIX\fP\|] -[\|\fB\-f\fP\ \fIN\fP\|] -[\|\fB\-g\fP\ \fIN\fP\|] +[\|\fB\-f\fP\ \fIX\fP\|] +[\|\fB\-g\fP\|] [\|\fB\-h\fP\ \fIN\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-j\fP\ \fIfilename\fP\|] @@ -111,7 +111,7 @@ [\|\fB\-b\fP\ \fIN\fP\|] [\|\fB\-d\fP\ \fIstr\fP\|] [\|\fB\-e\fP\ \fIX\fP\|] -[\|\fB\-f\fP\ \fIN\fP\|] +[\|\fB\-f\fP\ \fIX\fP\|] [\|\fB\-g\ F\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-l\fP\ \fIstr\fP\|] @@ -157,7 +157,7 @@ [\|\fB\-b\fP\ \fIN\fP\|] [\|\fB\-d\fP\ \fIstr\fP\|] [\|\fB\-e\fP\ \fIX\fP\|] -[\|\fB\-f\fP\ \fIN\fP\|] +[\|\fB\-f\fP\ \fIX\fP\|] [\|\fB\-g\ F\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-l\fP\ \fIstr\fP\|] @@ -201,7 +201,7 @@ [\|\fB\-b\fP\ \fIN\fP\|] [\|\fB\-d\fP\ \fIstr\fP\|] [\|\fB\-e\fP\ \fIX\fP\|] -[\|\fB\-f\fP\ \fIN\fP\|] +[\|\fB\-f\fP\ \fIX\fP\|] [\|\fB\-g\ F\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-m\fP\ \fIN\fP\|] @@ -314,6 +314,7 @@ [\|\fB\-V\fP\|] [\|\fB\-W\fP\ \fIN\fP\|] [\|\fB\-X\fP\ \fIN\fP\|] +[\|\fB\-Y\fP\ \fIX\fP\|] [\|\fB\-Z\fP\ \fIN\fP\|] [\|\fB\-a\fP\ \fIN\fP\|] [\|\fB\-b\fP\ \fIN\fP\|] @@ -346,7 +347,6 @@ [\|\fB\-P\fP\ \fIN\fP\|] [\|\fB\-T\fP\|] [\|\fB\-U\fP\|] -[\|\fB\-V\fP\|] [\|\fB\-X\fP\ \fIN\fP\|] [\|\fB\-Y\fP\ \fIX\fP\|] [\|\fB\-Z\fP\ \fIN\fP\|] @@ -378,6 +378,7 @@ [\|\fB\-X\fP\ \fIN\fP\|] [\|\fB\-d\fP\ \fIstr\fP\|] [\|\fB\-e\fP\ \fIX\fP\|] +[\|\fB\-f\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-k\fP\ \fIfilename\fP\|] [\|\fB\-o\fP\ \fIfilename\fP\|] @@ -394,7 +395,7 @@ the blastn or blastp algorithm. Both sequences must be either nucleotides or proteins. .PP -\fBblast\fP compares a sequence against either a local database or a +\fBblast2\fP compares a sequence against either a local database or a second sequence; it incorporates most of the functionality of both \fBbl2seq\fP and \fBblastall\fP, but uses a semi-experimental new internal engine. @@ -481,20 +482,23 @@ Input sequences in the form of accession.version .TP \fB\-A\fP\ \fIN\fP (blastall, blastall_old, blastcl3, blastpgp, megablast) -Multiple Hits window size (default is 40 for blastpgp and 0 for other -commands, but blastall, blastall_old, and blastcl3 interpret 0 as 40 -for all programs but blastn and megablast) +Multiple Hits window size; generally defaults to 0 (for single-hit +extensions), but defaults to 40 when using discontiguous templates. .TP -\fB\-B\fP\ \fIN\fP (blast) -Produce on-the-fly tabular output: +\fB\-B\fP\ \fIN\fP (blast2) +Produce on-the-fly output: .RS .PD 0 .IP 0 none (default) .IP 1 -just offsets and quality values +table of offsets and quality values .IP 2 add sequence data +.IP 3 +text ASN.1 +.IP 4 +binary ASN.1 .PD .RE .TP @@ -504,12 +508,12 @@ \fB\-B\fP\ \fIfilename\fP (blastpgp) Input Alignment File for PSI-BLAST Restart .TP -\fB\-C\fP\ \fIX\fP (blast, blastall, blastall_old, blastcl3) -Use composition-based statistics for tblastn: +\fB\-C\fP\ \fIX\fP (blast2, blastall, blastall_old, blastcl3) +Use composition-based statistics for blastp or tblastn: .RS .PD 0 .IP "D or d" -Default (equivalent to F) +Default (equivalent to \fBT\fP) .IP "0, F, or f" No composition-based statistics .IP "1, T, or t" @@ -522,6 +526,12 @@ 2005, unconditionally .PD .RE +.RS +When enabling statistics in blastall, blastall_old, or blastcl3 (\fIi.e.\fP, +not blast2), appending \fBu\fP (case-insensitive) to the mode enables +use of unified p-values combining alignment and compositional p-values +in round 1 only. +.RE .TP \fB\-C\fP\ \fIfilename\fP (blastpgp) Output File for PSI-BLAST Checkpointing @@ -540,7 +550,7 @@ .PD .RE .TP -\fB\-D\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3) +\fB\-D\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3) Translate sequences in the database according to genetic code \fIN\fP in /usr/share/ncbi/data/gc.prt (default is 1; only applies to tblast*) .TP @@ -556,6 +566,10 @@ traditional BLAST output (default) .IP 3 tab-delimited one line format +.IP 4 +incremental text ASN.1 +.IP 5 +incremental binary ASN.1 .PD .RE .TP @@ -565,17 +579,17 @@ \fB\-E\fP\ \fIN\fP (bl2seq, blastcl3, megablast) Extending a gap costs \fIN\fP (-1 invokes default behavior) .TP -\fB\-E\fP\ \fIN\fP (blast, blastall, blastall_old) +\fB\-E\fP\ \fIN\fP (blast2, blastall, blastall_old) Extending a gap costs \fIN\fP (-1 invokes default behavior: non-affine if greedy, 2 otherwise) .TP \fB\-E\fP\ \fIN\fP (blastpgp, impala, seedtop) Extending a gap costs \fIN\fP (default is 1) .TP -\fB\-F\fP\ \fIstr\fP (bl2seq, blast, blastall, blastall_old, blastpgp, +\fB\-F\fP\ \fIstr\fP (bl2seq, blast2, blastall, blastall_old, blastpgp, blastcl3, impala, megablast, rpsblast) Filter options for DUST or SEG; defaults to \fBT\fP for bl2seq, -blast, blastall, blastall_old, blastcl3, and megablast, and to +blast2, blastall, blastall_old, blastcl3, and megablast, and to \fBF\fP for blastpgp, impala, and rpsblast. .TP \fB\-F\fP (seedtop) @@ -584,14 +598,14 @@ \fB\-G\fP\ \fIN\fP (bl2seq, blastcl3, megablast) Opening a gap costs \fIN\fP (-1 invokes default behavior) .TP -\fB\-G\fP\ \fIN\fP (blast, blastall, blastall_old) +\fB\-G\fP\ \fIN\fP (blast2, blastall, blastall_old) Opening a gap costs \fIN\fP (-1 invokes default behavior: non-affine if greedy, 5 if using dynamic programming) .TP \fB\-G\fP\ \fIN\fP (blastpgp, impala, seedtop) Opening a gap costs \fIN\fP (default is 11) .TP -\fB\-H\fP (blast) +\fB\-H\fP (blast2) Produce HTML output .TP \fB\-H\fP\ \fIN\fP (blastpgp) @@ -603,7 +617,7 @@ \fB\-H\fP\ \fIN\fP (megablast) Maximal number of HSPs to save per database sequence (default is 0, unlimited) .TP -\fB\-I\fP\ \(dq\fIstart\ stop\fP\(dq (bl2seq, blast) +\fB\-I\fP\ \(dq\fIstart\ stop\fP\(dq (bl2seq, blast2) Location on first (query) sequence (applies only if file specified with \fB-i\fP contains a single sequence) .TP @@ -611,7 +625,7 @@ rpsblast, seedtop) Show GIs in deflines .TP -\fB\-J\fP\ \(dq\fIstart\ stop\fP\(dq (bl2seq, blast) +\fB\-J\fP\ \(dq\fIstart\ stop\fP\(dq (bl2seq, blast2) Location on second (subject) sequence (applies only if file specified with \fB-j\fP contains a single sequence) .TP @@ -619,25 +633,25 @@ rpsblast, seedtop) Believe the query defline .TP -\fB\-K\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp) +\fB\-K\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3, blastpgp) Number of best hits from a region to keep (off by default, if used a value of 100 is recommended) .TP -\fB\-L\fP (blast) +\fB\-L\fP (blast2) Use (classical Mega BLAST) lookup table with width 12 .TP \fB\-L\fP\ \fIstart,stop\fP (blastall, blastall_old, blastcl3, megablast, rpsblast) Location on query sequence (for rpsblast, only valid in blastp mode) .TP -\fB\-M\fP\ \fIstr\fP (bl2seq, blast, blastall, blastall_old, blastcl3, +\fB\-M\fP\ \fIstr\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, blastpgp, impala, seedtop) Use matrix \fIstr\fP (default = BLOSUM62) .TP \fB\-M\fP\ \fIN\fP (megablast) Maximal total length of queries for a single search (default = 5000000) .TP -\fB\-N\fP (blast) +\fB\-N\fP (blast2) Show only accessions for sequence IDs in tabular output .TP \fB\-N\fP\ \fIX\fP (blastpgp, rpsblast) @@ -662,7 +676,7 @@ blastpgp, impala, rpsblast, and seedtop with \fB\-J\fP, and only valid for megablast with \fB\-D2\fP. .TP -\fB\-P\fP\ \fIX\fP (blast) +\fB\-P\fP\ \fIX\fP (blast2) Identity percentage cut-off .TP \fB\-P\fP\ \fIN\fP (blastall, blastall_old, blastcl3, blastpgp, rpsblast) @@ -675,7 +689,7 @@ \fB\-P\fP\ \fIN\fP (megablast) Maximal number of positions for a hash value (set to 0 [default] to ignore) .TP -\fB\-Q\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3) +\fB\-Q\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3) Translate query according to genetic code \fIN\fP in /usr/share/ncbi/data/gc.prt (default is 1) .TP @@ -685,7 +699,7 @@ \fB\-Q\fP\ \fIfilename\fP (megablast) Masked query output; requires \fB-D\ 2\fP .TP -\fB\-R\fP (blast) +\fB\-R\fP (blast2) Compute locally optimal Smith-Waterman alignments. (This option is only available for gapped tblastn.) .TP @@ -701,7 +715,7 @@ \fB\-R\fP (megablast) Report the log information at the end of output .TP -\fB\-S\fP\ \fIN\fP (bl2seq, blast, blastall, blastall_old, blastcl3, +\fB\-S\fP\ \fIN\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, megablast) Query strands to search against database for blastn, blastx, tblastx: .RS @@ -725,7 +739,7 @@ rpsblast) Produce HTML output .TP -\fB\-T\fP\ \fIN\fP (blast) +\fB\-T\fP\ \fIN\fP (blast2) Type of a discontiguous word template: .RS .PD 0 @@ -742,13 +756,13 @@ rpsblast) Use lower case filtering for the query sequence .TP -\fB\-V\fP (bl2seq, blastall, megablast, rpsblast) +\fB\-V\fP (bl2seq, blastall, megablast) Force use of legacy engine .TP -\fB\-V\fP (blast) +\fB\-V\fP (blast2) Use variable word size approach to database scanning .TP -\fB\-W\fP\ \fIN\fP (bl2seq, blast, blastall, blastall_old, blastcl3, +\fB\-W\fP\ \fIN\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, blastpgp, megablast, rpsblast) Use words of size \fIN\fP (length of best perfect match; zero invokes default behavior, except with megablast, which defaults to 28, and @@ -756,7 +770,7 @@ commands vary with "program": 11 for blastn, 28 for megablast, and 3 for everything else.) .TP -\fB\-X\fP\ \fIN\fP (bl2seq, blast, blastall, blastall_old, blastcl3, +\fB\-X\fP\ \fIN\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, blastpgp, megablast, rpsblast, seedtop) X dropoff value for gapped alignment (in bits) (zero invokes default behavior, except with megablast, which defaults to 20, and rpsblast @@ -764,28 +778,28 @@ commands vary with "program": 30 for blastn, 20 for megablast, 0 for tblastx, and 15 for everything else.) .TP -\fB\-Y\fP\ \fIX\fP (bl2seq, blast, blastall, blastall_old, blastcl3, -blastpgp, rpsblast) +\fB\-Y\fP\ \fIX\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, +blastpgp, megablast, rpsblast) Effective length of the search space (use zero for the real size) .TP -\fB\-Z\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-Z\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, megablast, rpsblast) X dropoff value for final [dynamic programming?] gapped alignment in bits (default is 50 for blastn and megablast, 0 for tblastx, 25 for others) .TP \fB\-a\fP\ \fIfilename\fP (bl2seq) -Write SeqAnnot output to \fIfilename\fP +Write text ASN.1 output to \fIfilename\fP .TP -\fB\-a\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-a\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast) Number of threads to use (default is one) .TP -\fB\-b\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-b\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast) Number of database sequences to show alignments for (B) (default is 250) .TP -\fB\-c\fP (blast) +\fB\-c\fP (blast2) Mask lower case .TP \fB\-c\fP\ \fIN\fP (blastpgp, impala) @@ -794,9 +808,9 @@ \fB\-d\fP\ \fIN\fP (bl2seq) Use theoretical DB size of \fIN\fP (zero stands for the real size) .TP -\fB\-d\fP\ \fIstr\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-d\fP\ \fIstr\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, seedtop) -Database to use (default is nr for all executables except blast, +Database to use (default is nr for all executables except blast2, which requires a second FASTA sequence if this is not set) .TP \fB\-d\fP\ \fIfilename\fP (rpsblast) @@ -805,7 +819,7 @@ \fB\-e\fP\ \fIX\fP Expectation value (E) (default = 10.0) .TP -\fB\-f\fP\ \fIN\fP (blastall, blastall_old, blastcl3) +\fB\-f\fP\ \fIX\fP (blast2, blastall, blastall_old, blastcl3) Threshold for extending hits, default if zero: 0 for blastn and megablast, 11 for blastp, 12 for blastx, and 13 for tblasn and tblastx. @@ -816,29 +830,20 @@ \fB\-f\fP (megablast) Show full IDs in the output (default - only GIs or accessions) .TP +\fB\-f\fP (seedtop) +Force searching for patterns even if they are too likely +.TP \fB\-g\ F\fP (bl2seq, blastall, blastall_old, blastcl3) Do not perform gapped alignment (N/A for tblastx) .TP -\fB\-g\fP\ \fIN\fP (blast) -Use greedy algorithm for gapped extensions: -.RS -.PD 0 -.IP 0 -no (default) -.IP 1 -one-step -.IP 2 -two-step -.IP 3 -two-step with ungapped -.PD -.RE +\fB\-g\fP (blast2) +Use greedy algorithm for gapped extensions .TP \fB\-g\ F\fP (megablast) -Generate words for every fourth base of the database (only relevant -for discontiguous words) +Make discontiguous megablast generate words for every base of the +database (mandatory with the current BLAST engine) .TP -\fB\-h\fP\ \fIN\fP (blast) +\fB\-h\fP\ \fIN\fP (blast2) Frame shift penalty for out-of-frame gapping (blastx, tblastn only; default is zero) .TP @@ -850,13 +855,13 @@ Read (first, query) sequence or set from \fIfilename\fP (default is stdin; not needed for blastpgp if restarting from scoremat) .TP -\fB\-j\fP\ \fIfilename\fP (bl2seq, blast) +\fB\-j\fP\ \fIfilename\fP (bl2seq, blast2) Read second (subject) sequence or set from \fIfilename\fP .TP \fB\-j\fP\ \fIN\fP (blastpgp) Maximum number of passes to use in multipass version (default = 1) .TP -\fB\-k\fP\ \fIstr\fP (blast) +\fB\-k\fP\ \fIstr\fP (blast2) Pattern for PHI-BLAST .TP \fB\-k\fP\ \fIfilename\fP (blastpgp, seedtop) @@ -871,7 +876,7 @@ \fB\-m\fP (bl2seq) Use Mega Blast for search .TP -\fB\-m\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-m\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast) alignment view options: .RS @@ -903,7 +908,7 @@ .PD .RE .TP -\fB\-n\fP (blast) +\fB\-n\fP (blast2) Show GIs in sequence IDs .TP \fB\-n\fP (blastall, blastall_old, blastcl3) @@ -915,7 +920,7 @@ \fB\-o\fP\ \fIfilename\fP Write final alignment report to \fIfilename\fP rather than stdout .TP -\fB\-p\fP\ \fIstr\fP (bl2seq, blast, blastall, blastall_old, blastcl3) +\fB\-p\fP\ \fIstr\fP (bl2seq, blast2, blastall, blastall_old, blastcl3) Use the "program" (comparison type) \fIstr\fP. The \fBDESCRIPTION\fP section covers this option in more detail. .TP @@ -939,7 +944,7 @@ .PD .RE .TP -\fB\-q\fP\ \fIN\fP (bl2seq, blast, blastall, blastall_old, blastcl3, +\fB\-q\fP\ \fIN\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, megablast, seedtop) Penalty for a nucleotide mismatch (blastn only) (default = -10 for seedtop, -3 for everything else) @@ -957,14 +962,13 @@ .PD .RE .TP -\fB\-r\fP\ \fIN\fP (bl2seq, blast, blastall, blastall_old, blastcl3, +\fB\-r\fP\ \fIN\fP (bl2seq, blast2, blastall, blastall_old, blastcl3, megablast, seedtop) Reward for a nucleotide match (blastn only) (default = 10 for seedtop, -10 for everything else) .TP -\fB\-s\fP (blast) -Generate words for every base of the database (default is every 4th; -may only be used with discontiguous words) +\fB\-s\fP (blast2) +No-op (formerly requested generating words for every base of the database) .TP \fB\-s\fP (blastall, blastall_old, blastcl3, blastpgp) Compute locally optimal Smith-Waterman alignments. @@ -974,7 +978,7 @@ \fB\-s\fP\ \fIN\fP (megablast) Minimal hit score to report (0 for default behavior) .TP -\fB\-t\fP\ \fIN\fP (bl2seq, blast, blastall, blastall_old, blastcl3) +\fB\-t\fP\ \fIN\fP (bl2seq, blast2, blastall, blastall_old, blastcl3) Length of a discontiguous word template (the largest intron allowed in a translated nucleotide sequence when linking multiple distinct assignments; default = 0; negative values disable linking for blastall, @@ -1005,7 +1009,7 @@ \fB\-t\fP\ \fIN\fP (megablast) Length of a discontiguous word template (contiguous word if 0 [default]) .TP -\fB\-u\fP (blast) +\fB\-u\fP (blast2) Do only ungapped alignment (always TRUE for tblastx) .TP \fB\-u\fP\ \fIstr\fP (blastcl3) @@ -1024,18 +1028,18 @@ .PD .RE .TP -\fB\-v\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-v\fP\ \fIN\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast) Number of one-line descriptions to show (V) (default = 500) .TP -\fB\-w\fP\ \fIN\fP (blast) +\fB\-w\fP\ \fIN\fP (blast2) Window size (max. allowed distance between a pair of initial hits; 0 invokes default behavior, -1 turns off multiple hits) .TP \fB\-w\fP\ \fIN\fP (blastall, blastall_old, blastcl3) Frame shift penalty (OOF algorithm for blastx) .TP -\fB\-y\fP\ \fIX\fP (blast, blastall, blastall_old, blastcl3, blastpgp, +\fB\-y\fP\ \fIX\fP (blast2, blastall, blastall_old, blastcl3, blastpgp, impala, rpsblast) X dropoff for ungapped extensions in bits (0.0 invokes default behavior: 20 for blastn, 10 for megablast, and 7 for all others.) @@ -1043,7 +1047,7 @@ \fB\-y\fP\ \fIN\fP (megablast) X dropoff value for ungapped extension (default is 10) .TP -\fB\-z\fP\ \fIN\fP (blast) +\fB\-z\fP\ \fIN\fP (blast2) Longest intron length for uneven gap HSP linking (tblastn only; default is 0) .TP --- ncbi-tools6-6.1.20070822.orig/doc/man/asn2all.1 +++ ncbi-tools6-6.1.20070822/doc/man/asn2all.1 @@ -1,4 +1,4 @@ -.TH ASN2ALL 1 2005-05-16 NCBI "NCBI Tools User's Manual" +.TH ASN2ALL 1 2007-09-08 NCBI "NCBI Tools User's Manual" .SH NAME asn2all \- generate reports from ASN.1 biological data .SH SYNOPSIS @@ -14,6 +14,7 @@ [\|\fB\-f\fP\ \fIformat\fP\|] [\|\fB\-h\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] +[\|\fB\-k\fP\|] [\|\fB\-l\fP\|] [\|\fB\-n\fP\ \fIpolicy\fP\|] [\|\fB\-o\fP\ \fIfilename\fP\|] @@ -130,6 +131,9 @@ \fB\-i\fP\ \fIfilename\fP Input file name (standard input by default) .TP +\fB\-k\fP +Enable local fetching +.TP \fB\-l\fP Lock components in advance .TP --- ncbi-tools6-6.1.20070822.orig/doc/man/asn2idx.1 +++ ncbi-tools6-6.1.20070822/doc/man/asn2idx.1 @@ -1,12 +1,14 @@ -.TH ASN2IDX 1 2005-05-16 NCBI "NCBI Tools User's Manual" +.TH ASN2IDX 1 2007-09-08 NCBI "NCBI Tools User's Manual" .SH NAME asn2idx \- index ASN.1 Bioseq-sets for fast access to individual sequences .SH SYNOPSIS .B asn2idx [\|\fB\-\fP\|] [\|\fB\-b\fP\|] -[\|\fB\-d\fP\ \fIstr\fP\|] -\fB\-p\fP\ \fIstr\fP +[\|\fB\-d\fP\ \fIdir\fP\|] +[\|\fB\-f\fP\ \fIfilter\fP\|] +\fB\-p\fP\ \fIpath\fP +[\|\fB\-r\fP\ \fIpath\fP\|] [\|\fB\-t\fP\|] [\|\fB\-x\fP\ \fIstr\fP\|] .SH DESCRIPTION @@ -23,17 +25,23 @@ \fB\-b\fP Bioseq-sets are Binary .TP -\fB\-d\fP\ \fIstr\fP +\fB\-d\fP\ \fIdir\fP Required Subdirectory .TP -\fB\-p\fP\ \fIstr\fP +\fB\-f\fP\ \fIfilter\fP +Filter (default = \fBgbcon,gbest,gbgss,gbsts\fP) +.TP +\fB\-p\fP\ \fIpath\fP Path to Files .TP +\fB\-p\fP\ \fIpath\fP +Path for Results +.TP \fB\-t\fP Recurse .TP \fB\-x\fP\ \fIstr\fP -File Selection Substring (default = .aso) +File Selection Substring (default = \fB.aso\fP) .SH AUTHOR The National Center for Biotechnology Information. .SH SEE ALSO --- ncbi-tools6-6.1.20070822.orig/doc/man/asnval.1 +++ ncbi-tools6-6.1.20070822/doc/man/asnval.1 @@ -1,4 +1,4 @@ -.TH ASNVAL 1 2006-05-29 NCBI "NCBI Tools User's Manual" +.TH ASNVAL 1 2007-09-08 NCBI "NCBI Tools User's Manual" .SH NAME asnval \- validate ASN.1 biological sequence records .SH SYNOPSIS @@ -11,16 +11,19 @@ [\|\fB\-J\fP\|] [\|\fB\-L\fP\ \fIfilename\fP\|] [\|\fB\-M\fP\|] +[\|\fB\-N\fP\ \fIflags\fP\|] [\|\fB\-P\fP\ \fIN\fP\|] [\|\fB\-Q\fP\ \fIN\fP\|] [\|\fB\-R\fP\ \fIN\fP\|] [\|\fB\-S\fP\ \fIN\fP\|] [\|\fB\-T\fP\|] +[\|\fB\-X\fP\|] [\|\fB\-Y\fP\|] [\|\fB\-Z\fP\|] [\|\fB\-a\fP\ \fItype\fP\|] [\|\fB\-b\fP\|] [\|\fB\-c\fP\|] +[\|\fB\-d\fP\ \fIpath\fP\|] [\|\fB\-e\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-k\fP\|] @@ -61,6 +64,21 @@ \fB\-M\fP Match locus_tag against General ID .TP +\fB\-N\fP\ \fIflags\fP +Latitude-longitude / country flags +.RS +.PD 0 +.IP 0 +none +.IP 1 +test state/province +.IP 2 +ignore water exception +.IP 3 +both of the above +.PD +.RE +.TP \fB\-P\fP\ \fIN\fP Highest severity for error to show: .RS @@ -90,6 +108,9 @@ \fB\-T\fP Use Threads .TP +\fB\-X\fP +Exon splice check +.TP \fB\-Y\fP Check against old IDs .TP @@ -123,6 +144,9 @@ \fB\-c\fP Batch file is Compressed .TP +\fB\-d\fP\ \fIpath\fP +Path to Indexed Binary ASN.1 Data +.TP \fB\-e\fP Ignore transcription/translation Exceptions .TP @@ -139,7 +163,7 @@ Single output file .TP \fB\-p\fP\ \fIpath\fP -Path to ASN.1 Files [String] +Path to ASN.1 Files .TP \fB\-r\fP Remote Fetching from ID @@ -155,4 +179,5 @@ .SH AUTHOR The National Center for Biotechnology Information. .SH SEE ALSO +.BR cleanasn (1), .BR sequin (1). --- ncbi-tools6-6.1.20070822.orig/doc/man/idfetch.1 +++ ncbi-tools6-6.1.20070822/doc/man/idfetch.1 @@ -1,4 +1,4 @@ -.TH IDFETCH 1 2005-06-24 NCBI "NCBI Tools User's Manual" +.TH IDFETCH 1 2006-10-20 NCBI "NCBI Tools User's Manual" .SH NAME idfetch \- retrieve biological data from the NCBI ID1 server .SH SYNOPSIS @@ -30,7 +30,7 @@ .TP \fB\-F\fP\ \fIstr\fP Add the specified feature types (comma-delimited); allowed values are -CDD, SNP, SNP_graph, MGC, HPRD, and STS. +CDD, SNP, SNP_graph, MGC, HPRD, STS, tRNA, and microRNA. .TP \fB\-G\fP\ \fIfilename\fP File with list of GIs, (versioned) accessions, FASTA SeqID's to dump --- ncbi-tools6-6.1.20070822.orig/doc/firewall.html +++ ncbi-tools6-6.1.20070822/doc/firewall.html @@ -132,7 +132,8 @@

To see what ports are currently on, and their status, as reported within -NCBI, please refer to the following Firewall +NCBI, please refer to the following +Firewall Daemon Presence Check page. Ports marked INTERNAL are for NCBI use only and may be inaccessible from your site without, however, affecting availability of any services that NCBI provides. @@ -160,7 +161,7 @@

There is also an auxiliary UNIX shell script -fwd_check.sh to check all of the above +fwd_check.sh to check all of the above addresses.

--- ncbi-tools6-6.1.20070822.orig/make/makeall.unx +++ ncbi-tools6-6.1.20070822/make/makeall.unx @@ -1,4 +1,4 @@ -# makefile for asntool and ncbi core routines, +# -*- makefile -*- for asntool and ncbi core routines, # # $Id: makeall.unx,v 6.286 2007/08/03 12:42:48 lavr Exp $ # @@ -233,7 +233,7 @@ dlgutil1.c dlgutil2.c e2trmlst.c e2docsum.c asn2graphic.c \ medview.c bspview.c gbfview.c gphview.c gphdraw.c gxydraw.c gtrdraw.c \ seqpanel.c ingengraph.c ingenext.c ingenwin.c \ - biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c salogif.c + biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c SRC45 = ddvclick.c ddvgraph.c ddvopen.c ddvpanel.c @@ -384,7 +384,7 @@ dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o \ medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o \ seqpanel.o ingengraph.o ingenext.o ingenwin.o \ - biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o salogif.o + biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o OBJ45 = ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o @@ -481,7 +481,7 @@ nocopy : sources $(THR_OBJ) $(LIB1) $(LIB2) $(LIB3) $(DLIB4) $(DLIB400) \ $(LIB5) $(DLIB20) $(DLIB45) $(LIB22) $(LIB23) $(LIBCOMPADJ) \ $(DLIB28) $(DLIB30) $(DLIB3000) \ - $(DLIB34) $(DLIB37) $(DLIB38) $(LIB50) $(LIB60) $(LIB61) $(NCBI_SHLIBS) + $(DLIB34) $(DLIB37) $(DLIB38) $(LIB60) $(LIB61) $(NCBI_SHLIBS) sources : $(THR_SRC) $(SRC1) $(SRC2) $(SRC3) $(SRC4) $(SRC5) $(SRC20) $(SRC22) \ $(SRC23) $(SRC28) $(SRC30) $(SRC50) $(SRC60) $(SRC61) $(SRCCOMPADJ) @@ -489,7 +489,7 @@ ## To clean out the directory without removing make ## clean : - -rm -f *.[acho] + -rm -f *.[acho] *.glo .NO_PARALLEL: copy $(ULIB4) $(ULIB30) @@ -647,10 +647,12 @@ cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS) rm -f ../shlib/*.a -# -# Linux shared libs are built the same in the same manner as for SGI -# -shlib.lnx : shlib.sgi +shlib.lnx : + -mkdir ../shlib + -rm -f ../shlib/*.a + ln $(NCBI_LIBDIR)/*.a ../shlib + cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so.$(NCBI_VERSION_MAJOR)/"` SH1="$(CC) -o" SH2="-shared *.o" + rm -f ../shlib/*.a shlib.sgi : -mkdir ../shlib @@ -771,7 +773,7 @@ cp -fp ../algo/blast/core/*.h ../include/algo/blast/core - mkdir -p ../include/algo/blast/composition_adjustment $(SRCCOPY) ../algo/blast/composition_adjustment/*.c . - $(SRCCOPY) ../algo/blast/composition_adjustment/*.h ../include +# $(SRCCOPY) ../algo/blast/composition_adjustment/*.h ../include cp -fp ../algo/blast/composition_adjustment/*.h \ ../include/algo/blast/composition_adjustment - mkdir -p ../include/algo/blast/api --- ncbi-tools6-6.1.20070822.orig/make/makedemo.unx +++ ncbi-tools6-6.1.20070822/make/makedemo.unx @@ -1,4 +1,4 @@ -# makefile for demo programs +# -*- makefile -*- for demo programs # # $Id: makedemo.unx,v 6.87 2006/11/16 15:36:19 coulouri Exp $ # @@ -215,7 +215,7 @@ # fa2htgs fa2htgs : fa2htgs.c - $(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) $(OTHERLIBS) # cdscan --- ncbi-tools6-6.1.20070822.orig/make/makeshlb.unx +++ ncbi-tools6-6.1.20070822/make/makeshlb.unx @@ -1,4 +1,4 @@ -# +# -*- makefile -*- # # $Id: makeshlb.unx,v 6.1 1999/03/18 17:31:11 beloslyu Exp $ # @@ -12,7 +12,91 @@ SH2 = `lorder *.o | tsort` $(NCBI_OTHERLIBS) %.so: %.a - rm -f *.o __* + rm -f *.o *.glo __* ar x $< + case $< in \ + *OGL.a) for f in *.glo; do mv $$f `basename $$f .glo`.o; done ;; \ + esac $(SH1) $@ $(SH2) rm -f *.o __* + +so=so.$(NCBI_VERSION_MAJOR).$(NCBI_VERSION_MINOR) + +%.$(so): %.a + $(CC) -shared -Wl,-soname=$*.so.$(NCBI_VERSION_MAJOR) -o $@ \ + -Wl,--whole-archive $< -Wl,--no-whole-archive \ + $($*_deps) $($*_sysdeps) + +%.so.$(NCBI_VERSION_MAJOR): %.$(so) + ln -s $< $@ + ln -s $< $*.so + +# Make libncbiCacc and libncbiacc pointers to libncbiNacc, since it's +# the most useful variant in the usual (net-only) case. Do the same +# for libnetentr, and link the static version into libncbiNacc.so, due +# to a circular dependency. +libnetentr.$(so) libncbiCacc.$(so) libncbiacc.$(so): + ln -s libncbiNacc.$(so) $@ + +# Standardize on the OpenGL-enabled versions of Vibrant, since there's +# no longer any real penalty in doing so. +libvibrant.$(so): + ln -s libvibrantOGL.$(so) $@ +libncbicn3d.$(so): + ln -s libncbicn3dOGL.$(so) $@ + +libblast_deps = libblastcompadj.$(so) libncbi.$(so) +libblastapi_deps = libblast.$(so) libncbitool.$(so) +libblastcompadj_sysdeps = -lm +libncbi_sysdeps = -lm +# libncbiCacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so) +libncbiNacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so) +# libncbiacc_deps = libncbicdr.$(so) +libncbicdr_deps = libncbiobj.$(so) +libncbiid1_deps = libncbiobj.$(so) libnetcli.$(so) +libncbimla_deps = libncbiobj.$(so) libnetcli.$(so) +libncbimmdb_deps = libncbiid1.$(so) libncbitool.$(so) +libncbiobj_deps = libncbi.$(so) +libncbitool_deps = libblastcompadj.$(so) libncbiobj.$(so) +libncbitxc2_deps = libncbitool.$(so) libnetcli.$(so) +libnetblast_deps = libncbitool.$(so) libnetcli.$(so) +libnetcli_deps = libncbi.$(so) +# libnetentr_deps = libncbiacc.$(so) libnetcli.$(so) + +libddvlib_deps = libncbidesk.$(so) +libncbicn3d_deps = libncbiNacc.$(so) libddvlib.$(so) +libncbicn3dOGL_deps = $(libncbicn3d_deps) libvibrantOGL.$(so) +libncbidesk_deps = libblastapi.$(so) libncbimmdb.$(so) libvibrantOGL.$(so) +libvibgif_deps = libncbi.$(so) +libvibnet_deps = libncbiNacc.$(so) libncbidesk.$(so) +# libvibrant_deps = libncbi.$(so) +# libvibrant_sysdeps = $(VIBLIBS) +# for ddvcolor stuff +libvibrantOGL_deps = libncbiobj.$(so) +libvibrantOGL_sysdeps = $(OGLLIBS) $(VIBLIBS) + +# XXX - is there a way to express these programmatically? +libblast.$(so): $(libblast_deps) +libblastapi.$(so): $(libblastapi_deps) +# libncbiCacc.$(so): $(libncbiCacc_deps) +libncbiNacc.$(so): $(libncbiNacc_deps) +# libncbiacc.$(so): $(libncbiacc_deps) +libncbicdr.$(so): $(libncbicdr_deps) +libncbiid1.$(so): $(libncbiid1_deps) +libncbimla.$(so): $(libncbimla_deps) +libncbimmdb.$(so): $(libncbimmdb_deps) +libncbiobj.$(so): $(libncbiobj_deps) +libncbitool.$(so): $(libncbitool_deps) +libncbitxc2.$(so): $(libncbitxc2_deps) +libnetblast.$(so): $(libnetblast_deps) +libnetcli.$(so): $(libnetcli_deps) +# libnetentr.$(so): $(libnetentr_deps) + +libddvlib.$(so): $(libddvlib_deps) +# libncbicn3d.$(so): $(libncbicn3d_deps) +libncbicn3dOGL.$(so): $(libncbicn3dOGL_deps) +libncbidesk.$(so): $(libncbidesk_deps) +libvibgif.$(so): $(libvibgif_deps) +libvibnet.$(so): $(libvibnet_deps) +# libvibrant.$(so): $(libvibrant_deps) +libvibrantOGL.$(so): $(libvibrantOGL_deps) --- ncbi-tools6-6.1.20070822.orig/make/makenet.unx +++ ncbi-tools6-6.1.20070822/make/makenet.unx @@ -1,4 +1,4 @@ -# makefile for network demo programs and network entrez +# -*- makefile -*- for network demo programs and network entrez # # $Id: makenet.unx,v 6.219 2007/04/18 15:52:34 kans Exp $ # test, ignore @@ -322,6 +322,8 @@ # objects & sources needed for versions of network demo programs +OBJCN3D = cn3dmain.o + OBJDDV = ddvmain.o OBJUDV = udvmain.o @@ -431,10 +433,12 @@ cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS) rm -f ../shlib/*.a -# -# Linux shared libs are built the same in the same manner as for SGI -# -shlib.lnx : shlib.sgi +shlib.lnx : + -mkdir ../shlib + -rm -f ../shlib/*.a + ln $(NCBI_LIBDIR)/*.a ../shlib + cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so.$(NCBI_VERSION_MAJOR)/"` SH1="$(CC) -o" SH2="-shared *.o" + rm -f ../shlib/*.a shlib.sgi : -mkdir ../shlib @@ -502,7 +506,7 @@ $(SRCCOPY) ../network/vibnet/*.h ../include $(SRCCOPY) ../cdromlib/*.h ../include -$(SRCCOPY) ../network/wwwblast/Src/*.c . - -$(SRCCOPY) ../network/wwwblast/Src/*.h ../include +# -$(SRCCOPY) ../network/wwwblast/Src/*.h ../include $(SRCCOPY) ../cdromlib/accentr.c . $(SRCCOPY) ../cdromlib/accutils.c . -$(SRCCOPY) ../sequin/*.* . @@ -904,6 +908,12 @@ ## +Cn3D : $(OBJCN3D) $(BENTREZLIBS) netentcf $(BLIB36) + $(CC) -o Cn3D $(LDFLAGS) $(OBJCN3D) $(LIB31) $(LIB3000) $(LIB20) $(LIB45) \ + $(LIB22) $(LIB41) $(LIB23) $(LIB8) $(LIB7) $(NETCLILIB) \ + $(LIB400) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) \ + $(OGLLIBS) + ddv : $(OBJDDV) $(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \ @@ -1160,11 +1170,11 @@ # 'query' program used as WWW Entrez server query : query.c sumutils.c $(BLIB27) $(BLIB25) $(BLIB22) - $(CC) -o query $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB5) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o query $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB41) $(LIB5) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS) # 'query' program used as WWW Entrez server Nquery : query.c sumutils.c $(BLIB27) $(BLIB25) $(BLIB22) $(BENTREZLIBS) - $(CC) -o Nquery $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o Nquery $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB41) $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS) # srchnt - pattern match REN search --- ncbi-tools6-6.1.20070822.orig/corelib/ncbienv.c +++ ncbi-tools6-6.1.20070822/corelib/ncbienv.c @@ -812,6 +812,8 @@ if (fp == NULL) { path[0] = '\0'; pth = getenv ("NCBI"); + if (pth == NULL) + pth = "/etc/ncbi"; if (pth != NULL) { Nlm_FileBuildPath(path, pth, str + 1); fp = Ncbienv_FileOpen (path, "r"); --- ncbi-tools6-6.1.20070822.orig/corelib/ncbimain.c +++ ncbi-tools6-6.1.20070822/corelib/ncbimain.c @@ -67,6 +67,7 @@ #pragma segment NlmSegA #endif +extern Nlm_Int2 Nlm_Main(void) __attribute__((weak)); /***************************************************************************** * @@ -95,7 +96,12 @@ /* Initialize connection library's logger, registry and lock */ CONNECT_Init(0); - retval = Nlm_Main(); + if (Nlm_Main) { + retval = Nlm_Main(); + } else { + ErrPost(0, 0, "Neither main nor Nlm_Main defined by program."); + retval = -1; + } NlmThreadJoinAll(); --- ncbi-tools6-6.1.20070822.orig/desktop/ingenwin.c +++ ncbi-tools6-6.1.20070822/desktop/ingenwin.c @@ -3114,7 +3114,7 @@ len++; } c = (Char)fgetc(fp); - if (c==EOF) { + if (c==(Char)EOF) { return NULL; } } --- ncbi-tools6-6.1.20070822.orig/desktop/bspview.c +++ ncbi-tools6-6.1.20070822/desktop/bspview.c @@ -2435,13 +2435,13 @@ } #endif #ifdef WIN_MOTIF - argv [0] = "netscape"; + argv [0] = "sensible-browser"; argv [1] = url; argv [2] = NULL; child = fork(); if(child == 0) { - if (execvp ("netscape", argv) == -1) { - Message (MSG_POST, "Unable to launch netscape"); + if (execvp ("sensible-browser", argv) == -1) { + Message (MSG_POST, "Unable to launch browser"); exit(-1); } } --- ncbi-tools6-6.1.20070822.orig/debian/man/Cn3D-3.0.1 +++ ncbi-tools6-6.1.20070822/debian/man/Cn3D-3.0.1 @@ -0,0 +1,26 @@ +.TH CN3D 1 2001-10-05 NCBI "NCBI Tools User's Manual" +.SH NAME +Cn3D \- a 3-dimensional viewer for biological molecules +.SH SYNOPSIS +.B Cn3D +[\|\fIfilename\fP\|] +.SH DESCRIPTION +This manual page documents briefly the \fBCn3D\fP command. +This manual page was written for the Debian GNU/Linux distribution +because the original program does not have a manual page. +.PP +\fBCn3D\fP is a helper application for your web browser that allows +you to view 3-dimensional structures from NCBI's Entrez retrieval +service. +.SH OPTIONS +.TP +\fIfilename\fP +Initially display the data in \fIfilename\fP. +.SH AUTHOR +This manual page was written by Aaron M. Ucko , +for the Debian GNU/Linux system (but may be used by others). +.SH SEE ALSO +.ad l +.BR ddv (1), +.BR udv (1), + --- ncbi-tools6-6.1.20070822.orig/debian/man/vibrate.1 +++ ncbi-tools6-6.1.20070822/debian/man/vibrate.1 @@ -0,0 +1,21 @@ +.TH VIBRATE 1 2001-10-05 Debian "NCBI Tools User's Manual" +.SH NAME +vibrate \- run a program with the Vibrant library preloaded +.SH SYNOPSIS +.B vibrate +[\|\fB\-\-help\fP\|] +.PP +.B vibrate +\fIprogram\fP +[\|\fIarguments\fP\|] +.SH DESCRIPTION +\fBvibrate\fP runs the specified program, which presumably uses the +NCBI C toolkit, with the Vibrant library preloaded. The main effect +of this preloading is that omitting arguments produces a dialog box +for setting parameters rather than a usage message. +.SH OPTIONS +.TP +\fB\-\-help\fP +Print usage message and exit. +.SH AUTHOR +Aaron M. Ucko --- ncbi-tools6-6.1.20070822.orig/debian/TODO +++ ncbi-tools6-6.1.20070822/debian/TODO @@ -0,0 +1,2 @@ +* Document sequin's options properly. +* Split blast.1 back up, preferably semi-automatically? --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.doc-base.sequin +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.doc-base.sequin @@ -0,0 +1,15 @@ +Document: sequin +Title: Sequin Quick Guide +Author: Jonathan Kans, Colombe Chappey, Jinghui Zhang, Tatiana + Tatusov, and James Ostell +Abstract: Sequin is a program designed to aid in the submission of + sequences to the GenBank, EMBL, and DDBJ sequence databases. It was + written at the National Center for Biotechnology Information, part of + the National Library of Medicine at the National Institutes of + Health. +Section: science + +Format: HTML +Index: /usr/share/doc/ncbi-tools-x11/sequin.htm +Files: /usr/share/doc/ncbi-tools-x11/images/* + --- ncbi-tools6-6.1.20070822.orig/debian/control +++ ncbi-tools6-6.1.20070822/debian/control @@ -0,0 +1,134 @@ +Source: ncbi-tools6 +Section: libdevel +Priority: optional +Maintainer: Aaron M. Ucko +Build-Depends: debhelper (>= 5), binutils (>= 2.14.90.0.7), lesstif2-dev, libxmu-dev (>= 1:1), libxt-dev (>= 1:1), libx11-dev (>= 2:1), libsm-dev (>= 1:1), libice-dev (>= 1:1), libxext-dev (>= 1:1), libpng12-dev | libpng-dev, libglu1-mesa-dev | libglu-dev, libgl1-mesa-dev | libgl-dev, tcsh | c-shell, libpcre3-dev, cdbs (>= 0.4.40), pmake, dpkg-dev (>= 1.13.19) +Build-Depends-Indep: icoutils, imagemagick +Standards-Version: 3.7.2 +Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/ + +Package: libncbi6 +Architecture: any +Section: libs +Depends: ${shlibs:Depends}, ncbi-data (= ${source:Version}) +Conflicts: ncbi-tools6 (<< 6.1.20030421-2), vibrant6 (<< 6.1.20030421-2), blast2 (<< 1:2.2.14), ncbi-tools-bin (<< 6.1.20060507-1), ncbi-tools-x11 (<< 6.1.20060507-1) +Replaces: ncbi-tools6 (<< 6.1.20030421-2), vibrant6 (<< 6.1.20030421-2) +Provides: ncbi-tools6 +Description: NCBI libraries for biology applications + The NCBI Software Development Toolkit was developed for the production and + distribution of GenBank, Entrez, BLAST, and related services by NCBI. It + allows you to read and write NCBI ASN.1 files, builds Blast or Entrez, etc. + +Package: libncbi6-dev +Architecture: any +Depends: libncbi6 (= ${binary:Version}) +Provides: ncbi-tools-dev, ncbi-tools6-dev +Conflicts: ncbi-tools-dev, menu (<< 2.1.8) +Replaces: ncbi-tools6-dev (<< 6.1.20030421-2), vibrant-dev (<< 6.1.20030421-2) +Description: NCBI libraries for biology applications (development files) + This package is for developers or people who want to compile programs + only. In addition to development headers and libraries, it contains the + utilities asntool and errhdr. + +Package: libncbi6-dbg +Architecture: any +Priority: extra +Depends: libncbi6 (= ${binary:Version}) +Recommends: gdb (>= 6.0) +Conflicts: ncbi-tools6-dbg +Replaces: ncbi-tools6-dbg +Provides: ncbi-tools6-dbg +Description: NCBI libraries for biology applications (debugging symbols) + This package is useful to provide a backtrace with symbol names in a + debugger; this facilitates interpretation of core dumps, and aids in finding + logic errors in programs using the libraries in this package (or the + libraries themselves). + . + Non-programmers will likely have little use for this package. See the + libncbi6 package for more information. + +Package: ncbi-data +Architecture: all +Section: libs +Replaces: ncbi-tools6 (<< 6.1.20011220a-1), libncbi6 (<< 6.1.20060507), libvibrant6 (<< 6.1.20060507) +Conflicts: ncbi-tools-bin (<< 6.1.20021119), blast2 (<< 6.1.20021119), vibrant6 (<< 6.1.20021119) +Description: Platform-independent data for the NCBI toolkit + This package contains support files needed by the NCBI toolkit on all + platforms. + +Package: ncbi-tools-bin +Architecture: any +Section: science +Depends: ${shlibs:Depends}, libncbi6 (<< ${source:Upstream-Version}.1) +Suggests: blast2, ncbi-tools-x11, libvibrant6a +Conflicts: menu (<< 2.1.8) +Description: NCBI libraries for biology applications (text-based utilities) + This package includes various utilities distributed with the NCBI C SDK. + None of the programs in this package require X; you can find the X-based + utilities in the ncbi-tools-x11 package. BLAST and related tools are + in a separate package (blast2). + +Package: ncbi-tools-x11 +Architecture: any +Section: science +Depends: ${shlibs:Depends}, libncbi6 (<< ${source:Upstream-Version}.1), libvibrant6a (<< ${source:Upstream-Version}.1), ncbi-tools-data (>= 6.1.20070822-2) +Suggests: blast2, ncbi-tools-bin +Replaces: libncbi6 (<< 6.1.20051206), ncbi-tools6 (<< 6.1.20030421-2) +Description: NCBI libraries for biology applications (X-based utilities) + This package includes some X-based utilities distributed with the + NCBI C SDK: Cn3D, Network Entrez, Sequin, ddv, and udv. These + programs are not part of ncbi-tools-bin because they depend on + several additional library packages. + +Package: blast2 +Architecture: any +Section: science +Depends: ${shlibs:Depends}, libncbi6 (<< ${source:Upstream-Version}.1) +Suggests: ncbi-tools-bin, ncbi-tools-x11, libvibrant6a +Conflicts: menu (<< 2.1.8) +Description: Basic Local Alignment Search Tool + The famous sequence alignment program. This is "official" NCBI version, + #2. The blastall executable allows you to give a nucleotide or protein + sequence to the program. It is compared against databases and a summary of + matches is returned to the user. + . + Note that databases are not included in Debian; they must be retrieved + manually. + +Package: libvibrant6a +Architecture: any +Section: libs +Depends: ${shlibs:Depends} +Replaces: vibrant6 (<< 6.1.20030421-2), libvibrant6, libvibrant6-gl, libvibrant6-nogl +Conflicts: libvibrant6, libvibrant6-gl, libvibrant6-nogl +Description: NCBI libraries for graphic biology applications + This is the library for those who just want to run Vibrant applications. + It also includes a wrapper (vibrate) that allows many NCBI applications to + provide a GUI for selecting options. + +Package: libvibrant6-dev +Architecture: any +Depends: libvibrant6a (= ${binary:Version}), libncbi6-dev (= ${binary:Version}), lesstif2-dev, libxmu-dev, libglu1-mesa-dev | libglu-dev, libgl1-mesa-dev | libgl-dev +Provides: vibrant-dev +Replaces: vibrant-dev (<< 6.1.20030421-2), libvibrant6-gl-dev, libvibrant6-nogl-dev +Description: NCBI libraries for graphic biology applications (development files) + Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic + biological applications. + +Package: libvibrant6a-dbg +Architecture: any +Priority: extra +Depends: libvibrant6a (= ${binary:Version}) +Recommends: gdb (>= 6.0) +Suggests: libncbi6-dbg (= ${binary:Version}) +Conflicts: vibrant6-dbg +Replaces: vibrant6-dbg +Provides: vibrant6-dbg +Description: NCBI libraries for graphic biology applications (unstripped) + This package is useful to provide a backtrace with symbol names in a + debugger; this facilitates interpretation of core dumps, and aids in finding + logic errors in programs using the libraries in this package (or the + libraries themselves). + . + Non-programmers will likely have little use for this package. See the + libvibrant6a package for more information. --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.doc-base.firewall +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.doc-base.firewall @@ -0,0 +1,11 @@ +Document: ncbi-tools-firewall +Title: Connecting to Network Entrez through a firewall +Author: The National Center for Biotechnology Information +Abstract: Some NCBI applications may need to be explicitly configured + to access NCBI network resources. This document explains how to do + that, even when there is a firewall in between. +Section: net + +Format: HTML +Index: /usr/share/doc/ncbi-tools-x11/firewall.html +Files: /usr/share/doc/ncbi-tools-x11/fire* --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.postinst +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.postinst @@ -0,0 +1,8 @@ +#!/bin/sh -e + +/usr/sbin/update-alternatives --install \ + /usr/bin/Cn3D Cn3D /usr/bin/Cn3D-3.0 30 \ + --slave /usr/share/man/man1/Cn3D.1.gz Cn3D.1.gz \ + /usr/share/man/man1/Cn3D-3.0.1.gz + +#DEBHELPER# --- ncbi-tools6-6.1.20070822.orig/debian/NOTES +++ ncbi-tools6-6.1.20070822/debian/NOTES @@ -0,0 +1,2 @@ +X apps should pull in -lvibrant BEFORE -lvibgif to avoid problematic +shadowing. --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6-dev.override +++ ncbi-tools6-6.1.20070822/debian/libncbi6-dev.override @@ -0,0 +1,2 @@ +libncbi6-dev: menu-icon-missing /usr/share/pixmaps/asntool.xpm +libncbi6-dev: menu-icon-missing /usr/share/pixmaps/ncbilogo.xpm --- ncbi-tools6-6.1.20070822.orig/debian/rules +++ ncbi-tools6-6.1.20070822/debian/rules @@ -0,0 +1,263 @@ +#!/usr/bin/make -f +include /usr/share/cdbs/1/rules/buildcore.mk +include /usr/share/cdbs/1/class/langcore.mk +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/rules/utils.mk + +DEB_DH_INSTALL_SOURCEDIR = debian/tmp +# The -V must be last here. +DEB_DH_MAKESHLIBS_ARGS_ALL = -V +DEB_INSTALL_CHANGELOGS_ALL = README +DEB_INSTALL_DOCS_ALL += -X.svn + +pkgroot = debian/$(cdbs_curpkg) +docdir = $(pkgroot)/usr/share/doc/$(cdbs_curpkg) + +export NCBI_VERSION_FULL=$(DEB_VERSION) +export NCBI_VERSION=$(word 1, $(subst -, ,$(NCBI_VERSION_FULL))) +export NCBI_VERSION_MAJOR=$(word 1, $(subst ., ,$(NCBI_VERSION))) +export NCBI_VERSION_MINOR=$(NCBI_VERSION:$(NCBI_VERSION_MAJOR).%=%) +export NCBI_VERSION_DATE =$(word 3, $(subst ., ,$(NCBI_VERSION))) +export NCBI_VERSION_DEBREL=$(word 2, $(subst -, ,$(NCBI_VERSION_FULL))) + +#export BLAST_VERSION=1:$(shell awk -F\" '/\#define BLAST_ENGINE_VERSION/ {print $$2}' tools/blastdef.h) +export BLAST_VERSION=1:$(shell cat demo/.BLAST_VERSION) +export BLAST_VERSION_DATED=$(BLAST_VERSION).$(NCBI_VERSION_DATE) +export BLAST_VERSION_FULL=$(BLAST_VERSION_DATED)-$(NCBI_VERSION_DEBREL) + +testversions: + env | fgrep NCBI_VERSION + env | fgrep BLAST_VERSION + +# Set these here, rather than using the csh hackage that passes for an +# upstream build system. Mostly taken from ../platform/{ppc,}linux.ncbi.mk. +# CC = gcc -pipe +VIBFLAG = -DWIN_MOTIF +VIBLIBS = -lXm -lXmu -lXt -lX11 # -lXext # -lXp +OTHERLIBS = -lm +RANLIB = ranlib +ifneq (,$(wildcard /usr/lib/libpthread.*)) +MT_OTHERLIBS = -lpthread +THREAD_OBJ = ncbithr.o +else +MT_OTHERLIBS = +THREAD_OBJ = +endif +NETENTREZVERSION = 2.02c2ASN1SPEC6 + +ifeq ($(DEB_HOST_ARCH),alpha) +CFLAGS += -mieee +endif + +OGL_TARGETS = Cn3D +OGL_LIBVARS = LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a +OGLLIBS = -lGLU -lGL + +PNG_INCLUDE = -D_PNG +PNG_LIBS = -lpng # -lz + +USESHLIB = NCBI_LINKINGLIBDIR="../shlib -L../lib" # Kludge. +MAKESHLIB = $(USESHLIB) NCBI_SHLIBS=shlib +# Controls how shared libraries are built; appropriate for ELF w/GNU tools. + +export NCBI_LBSM_SRC=ncbi_lbsmd_stub.c +export NCBI_LBSM_OBJ=ncbi_lbsmd_stub.o + +CURDIR := $(shell pwd) +ifeq ($(LD_LIBRARY_PATH),) +export LD_LIBRARY_PATH:=$(CURDIR)/shlib +else +export LD_LIBRARY_PATH:=$(CURDIR)/shlib:$(LD_LIBRARY_PATH) +endif + +# Apps which should be multithreaded if possible. +MTAPPS = blast blastall blastall_old blastpgp seedtop megablast rpsblast \ + blastclust + +VIB = Psequin sbtedit udv ddv blastcl3 idfetch bl2seq asn2gb tbl2asn \ + gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml asnval \ + cleanasn insdseqget nps2gps spidey trna2sap trna2tbl $(OGL_TARGETS) + +#OTHERS = others +OTHERS = libncbimla.a libnetblast.a libncbitxc2.a libncbiid1.a shlib + +COMMON_FLAGS = LCL=lnx CC="$(CC)" LDFLAGS1="$(CFLAGS)" RAN="$(RANLIB)" +COMMON_FLAGS += OTHERLIBS="$(OTHERLIBS)" VIBLIBS="$(VIBLIBS)" +COMMON_FLAGS += VIBFLAG="$(VIBFLAG)" + +ICONS = debian/asntool.xpm debian/ncbilogo.xpm + +# MAKE_IN_BULD = $(MAKE) -C build +MAKE_IN_BUILD = cd build && pmake + +common-configure-arch common-configure-indep:: debian/stamp-setup + +debian/stamp-setup: + cd build && ln -s ../make/*.unx . + ln -s ../make/ln-if-absent build + mv build/makeall.unx build/makefile + chmod +x debian/makemenu debian/installman + touch $@ + +common-build-arch:: debian/stamp-built + +debian/stamp-shlibs: +# $(MAKE_IN_BUILD) clean + + $(MAKE_IN_BUILD) all $(COMMON_FLAGS) $(USESHLIB) \ + CFLAGS1="-c $(CFLAGS) $(PNG_INCLUDE) -fPIC" \ + LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \ + LIB30=libncbicn3d.a LIB45=libddvlib.a $(OGL_LIBVARS) + $(MAKE_IN_BUILD) -f makenet.unx $(COMMON_FLAGS) $(USESHLIB) \ + CFLAGS1="-c $(CFLAGS) -fPIC" NETENTREZVERSION="$(NETENTREZVERSION)" \ + BLIB31=libvibnet.a OGLLIBS="$(OGLLIBS) $(PNG_LIBS)" all $(OTHERS) + touch $@ + +debian/stamp-built: debian/stamp-shlibs +# Clear out the PIC objects + $(MAKE_IN_BUILD) clean + + $(MAKE_IN_BUILD) all $(COMMON_FLAGS) $(USESHLIB) \ + CFLAGS1="-c $(CFLAGS) $(PNG_INCLUDE)" \ + LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \ + LIB30=libncbicn3d.a LIB45=libddvlib.a $(OGL_LIBVARS) +# Build demos without vibrant to avoid unnecessary dependencies; +# users who want the Vibrant UI can use vibrate(1). + $(MAKE_IN_BUILD) -f makedemo.unx $(COMMON_FLAGS) $(USESHLIB) \ + CFLAGS1="-c $(CFLAGS)" VIBLIBS= VIBFLAG= LIB50=-lpcre +ifneq (,$(wildcard /usr/lib/libpthread.*)) + -cd build && rm -f $(MTAPPS) +endif + $(MAKE_IN_BUILD) -f makedemo.unx $(COMMON_FLAGS) $(USESHLIB) \ + CFLAGS1="-c $(CFLAGS)" VIBLIBS= VIBFLAG= THREAD_OBJ="$(THREAD_OBJ)" \ + THREAD_OTHERLIBS="$(MT_OTHERLIBS)" $(MTAPPS) +# Don't bother passing OGLLIBS or VIBLIBS, which apps don't use directly. + $(MAKE_IN_BUILD) -f makenet.unx $(COMMON_FLAGS) $(USESHLIB) \ + CFLAGS1="-c $(CFLAGS)" THREAD_OBJ="$(THREAD_OBJ)" \ + THREAD_OTHERLIBS="$(MT_OTHERLIBS)" \ + NETENTREZVERSION="$(NETENTREZVERSION)" BLIB31=libvibnet.a \ + OGLLIBS= VIBLIBS= VIB="$(VIB)" +# date > VERSION + touch $@ + +clean:: + -rm -rf build/* bin/* include/* lib/* shlib + -rm -f debian/stamp-built debian/stamp-shlibs debian/stamp-setup + -rm -f debian/*.menu $(ICONS) + +common-install-arch:: +# $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp + install -d debian/tmp/usr/lib + install -m 644 lib/* shlib/*.so.$(NCBI_VERSION) debian/tmp/usr/lib + for x in ncbiacc ncbiCacc netentr; do \ + rm -f debian/tmp/usr/lib/lib$$x.so.$(NCBI_VERSION) && \ + ln -s libncbiNacc.so.$(NCBI_VERSION_MAJOR) \ + debian/tmp/usr/lib/lib$$x.so.$(NCBI_VERSION_MAJOR) && \ + ln -s libncbiNacc.so debian/tmp/usr/lib/lib$$x.so; \ + done + for x in ncbicn3d vibrant; do \ + rm -f debian/tmp/usr/lib/lib$$x.so.$(NCBI_VERSION) && \ + ln -s lib$${x}OGL.so.$(NCBI_VERSION_MAJOR) \ + debian/tmp/usr/lib/lib$$x.so.$(NCBI_VERSION_MAJOR) && \ + ln -s lib$${x}OGL.so debian/tmp/usr/lib/lib$$x.so; \ + done + rm -f debian/tmp/usr/lib/libregexp.* + cd debian/tmp/usr/lib && \ + for f in *.so.$(NCBI_VERSION); do \ + base=`basename $$f .so.$(NCBI_VERSION)` && \ + ln -s $$f $$base.so.$(NCBI_VERSION_MAJOR) && \ + ln -s $$f $$base.so; \ + done +# install -d debian/tmp/usr/lib/debug +# cp -a debian/tmp/usr/lib/*.so.* debian/tmp/usr/lib/debug + + install -d debian/tmp/usr/include/ncbi + cp -LRp include/* debian/tmp/usr/include/ncbi + cd debian/tmp/usr/include/ncbi && \ + rm -f FSpCompat.h FullPath.h More*.h Optimization*.h pcre*.h + find debian/tmp/usr/include -type f | xargs chmod 644 + + install -d debian/tmp/usr/bin + install `find build -type f -perm +111 -print` debian/tmp/usr/bin + rm -f debian/tmp/usr/bin/*test* + rm -f debian/tmp/usr/bin/*demo* +# Useless as a binary, and seems to be broken anyway + rm -f debian/tmp/usr/bin/dosimple +# Seems to be a functional version of sort(1) with no special features +# (but lacking some features of GNU sort) + rm -f debian/tmp/usr/bin/ncbisort +# Obsolete + rm -f debian/tmp/usr/bin/cdscan + rm -f debian/tmp/usr/bin/entrcmd +# install -d debian/tmp/usr/lib/cgi-bin +# mv debian/tmp/usr/bin/blast.REAL debian/tmp/usr/lib/cgi-bin + rm -f debian/tmp/usr/bin/blast.REAL + mv debian/tmp/usr/bin/Cn3D debian/tmp/usr/bin/Cn3D-3.0 +# mv debian/tmp/usr/bin/fmerge debian/tmp/usr/bin/fastamerge + mv debian/tmp/usr/bin/blast debian/tmp/usr/bin/blast2 + + debian/makemenu debian/ncbi-tools-x11.install + debian/makemenu -v debian/ncbi-tools-bin.install + debian/makemenu -v debian/libncbi6-dev.install + debian/makemenu -v debian/blast2.install + +binary-install/blast2:: + install -d $(pkgroot)/usr/share/man/man1 + debian/installman blast2 blast + +binary-install/libncbi6:: +# install -d $(docdir) + install -m 644 config/README $(docdir)/README.config + install -m 644 network/nsclilib/readme $(docdir)/README.net-cfg + +binary-install/ncbi-tools-bin:: +# install -d $(docdir) + install -m 644 doc/fa2htgs/README $(docdir)/README.fa2htgs + +binary-install/ncbi-tools-x11:: +# install -d $(docdir) + install -m 644 sequin/README $(docdir)/README.sequin + +$(patsubst %,binary-post-install/%,$(DEB_PACKAGES)) :: binary-post-install/%: + test ! -d $(pkgroot)/usr/bin || debian/installman $(cdbs_curpkg) + if test -f debian/$(cdbs_curpkg).override; then \ + dir=$(pkgroot)/usr/share/lintian/overrides && \ + install -d $$dir && \ + install -m 644 debian/$(cdbs_curpkg).override \ + $$dir/$(cdbs_curpkg); \ + fi + +common-binary-predeb-arch:: list-missing +# Also make sure there aren't any overlaps... + -for p in $(DEB_PACKAGES); do find debian/$$p/[^D]* -type f; done | \ + cut -d/ -f3- | sort | uniq -c -d + +debian/asntool.xpm: link/mswin/asntool.ico + convert $< $@ + +icon_in = link/mswin/ncbilogo.ico +hi = debian/ncbi-data/usr/share/icons/hicolor +lo = debian/ncbi-data/usr/share/icons/locolor + +debian/ncbilogo.xpm: $(icon_in) + icotool -x -w 32 -b 8 -o - $< | convert png:- $@ + + +binary-install/ncbi-data:: $(ICONS) + install -d debian/ncbi-data/etc/ncbi + install -m 644 debian/.*rc debian/ncbi-data/etc/ncbi + install -d debian/ncbi-data/usr/bin + install debian/vibrate debian/ncbi-data/usr/bin + install -d debian/ncbi-data/usr/share/ncbi/data + install -m 644 data/* debian/ncbi-data/usr/share/ncbi/data + install -d debian/ncbi-data/usr/share/pixmaps + install -m 644 $(ICONS) debian/ncbi-data/usr/share/pixmaps + for w in 16 32 48; do \ + d=$${w}x$${w} && \ + install -d $(lo)/$$d $(hi)/$$d && \ + icotool -x -w $$w -b 4 -o $(lo)/$$d/ncbilogo.png $(icon_in) && \ + icotool -x -w $$w -b 32 -o $(hi)/$$d/ncbilogo.png $(icon_in) \ + || exit 1 ; \ + done + +binary-makedeb-IMPL/blast2:: DEB_DH_GENCONTROL_ARGS=-- -v$(BLAST_VERSION_FULL) --- ncbi-tools6-6.1.20070822.orig/debian/watch +++ ncbi-tools6-6.1.20070822/debian/watch @@ -0,0 +1,4 @@ +version=3 +opts=uversionmangle=s/^/6.1./ \ + ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/(\d{8}) ncbi.tar.gz \ + debian uupdate --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6.dirs +++ ncbi-tools6-6.1.20070822/debian/libncbi6.dirs @@ -0,0 +1 @@ +/etc/ncbi --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6.docs +++ ncbi-tools6-6.1.20070822/debian/libncbi6.docs @@ -0,0 +1,5 @@ +README +README.htm +doc/FAQ.txt +doc/dispatcher.html +doc/ncbixml.txt --- ncbi-tools6-6.1.20070822.orig/debian/blast2.examples +++ ncbi-tools6-6.1.20070822/debian/blast2.examples @@ -0,0 +1 @@ +doc/blast/*.pl --- ncbi-tools6-6.1.20070822.orig/debian/blast2.doc-base +++ ncbi-tools6-6.1.20070822/debian/blast2.doc-base @@ -0,0 +1,14 @@ +Document: blast2 +Title: Basic Local Alignment Search Tool +Author: The National Center for Biotechnology Information +Abstract: The Basic Local Alignment Search Tool (BLAST) finds regions of + local similarity between sequences. The program compares nucleotide or + protein sequences to sequence databases and calculates the statistical + significance of matches. BLAST can be used to infer functional and + evolutionary relationships between sequences as well as help identify + members of gene families. +Section: science + +Format: HTML +Index: /usr/share/doc/blast2/index.html +Files: /usr/share/doc/blast2/*.html --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.override +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.override @@ -0,0 +1 @@ +ncbi-tools-x11: menu-icon-missing /usr/share/pixmaps/ncbilogo.xpm --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-bin.docs +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-bin.docs @@ -0,0 +1,2 @@ +doc/README.asn2xml +doc/gene2xml.txt --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6-dev.install +++ ncbi-tools6-6.1.20070822/debian/libncbi6-dev.install @@ -0,0 +1,199 @@ +usr/bin/asntool +usr/bin/errhdr +usr/include/ncbi/PubStructAsn.h +usr/include/ncbi/a2f*.h +usr/include/ncbi/acc*.h +usr/include/ncbi/actutils.h +usr/include/ncbi/algo +usr/include/ncbi/ali*.h +usr/include/ncbi/all.h +usr/include/ncbi/allpub.h +usr/include/ncbi/asn*.h +usr/include/ncbi/bandalgn.h +usr/include/ncbi/binary.h +usr/include/ncbi/bl*.h +usr/include/ncbi/bxmlobj.h +usr/include/ncbi/casn.h +usr/include/ncbi/cdconfig.h +usr/include/ncbi/cdd*.h +usr/include/ncbi/cdentrez.h +usr/include/ncbi/cdnewlib.h +usr/include/ncbi/cdrom*.h +usr/include/ncbi/codon.h +usr/include/ncbi/connect +usr/include/ncbi/corematx.h +usr/include/ncbi/ctools +usr/include/ncbi/db_list.h +usr/include/ncbi/ddvcolor.h +usr/include/ncbi/dotseq.h +usr/include/ncbi/dust.h +usr/include/ncbi/dvncode.h +usr/include/ncbi/edutil.h +usr/include/ncbi/egkludge.h +usr/include/ncbi/ent2api.h +usr/include/ncbi/errdefn.h +usr/include/ncbi/explore.h +usr/include/ncbi/fastadl.h +usr/include/ncbi/fdl*.h +usr/include/ncbi/ffprint.h +usr/include/ncbi/findrepl.h +usr/include/ncbi/ftusrstr.h +usr/include/ncbi/gapxdrop.h +usr/include/ncbi/gather.h +usr/include/ncbi/gb*.h +usr/include/ncbi/gifgen.h +usr/include/ncbi/id1*.h +usr/include/ncbi/id2*.h +usr/include/ncbi/jsavlt.h +usr/include/ncbi/jz*.h +usr/include/ncbi/list.h +usr/include/ncbi/lnfac.h +usr/include/ncbi/lookup.h +usr/include/ncbi/lsqfetch.h +usr/include/ncbi/mapcn3d.h +usr/include/ncbi/mapmime.h +usr/include/ncbi/mapmla.h +usr/include/ncbi/mapproj.h +usr/include/ncbi/mappubme.h +usr/include/ncbi/maputil.h +usr/include/ncbi/matrix.h +usr/include/ncbi/mb*.h +usr/include/ncbi/mconsist.h +usr/include/ncbi/mdrcherr.h +usr/include/ncbi/medarch.h +usr/include/ncbi/medutil.h +usr/include/ncbi/mimapi.h +usr/include/ncbi/mkbioseq.h +usr/include/ncbi/mla2api.h +usr/include/ncbi/mlkludge.h +usr/include/ncbi/mmdb*.h +usr/include/ncbi/ncbi.h +usr/include/ncbi/ncbibs.h +usr/include/ncbi/ncbienv.h +usr/include/ncbi/ncbierr.h +usr/include/ncbi/ncbifile.h +usr/include/ncbi/ncbilang.h +usr/include/ncbi/ncbilcl.h +usr/include/ncbi/ncbimain.h +usr/include/ncbi/ncbimath.h +usr/include/ncbi/ncbimem.h +usr/include/ncbi/ncbimisc.h +usr/include/ncbi/ncbimsg.h +usr/include/ncbi/ncbinet.h +usr/include/ncbi/ncbiopt.h +usr/include/ncbi/ncbiprop.h +usr/include/ncbi/ncbisam.h +usr/include/ncbi/ncbisami.h +usr/include/ncbi/ncbisgml.h +usr/include/ncbi/ncbisort.h +usr/include/ncbi/ncbisrti.h +usr/include/ncbi/ncbistd.h +usr/include/ncbi/ncbistr.h +usr/include/ncbi/ncbithr.h +usr/include/ncbi/ncbitime.h +usr/include/ncbi/ncbiwin.h +usr/include/ncbi/ncbiwww.h +usr/include/ncbi/needleman.h +usr/include/ncbi/netblap3.h +usr/include/ncbi/netcnfg.h +usr/include/ncbi/netentr.h +usr/include/ncbi/netlib.h +usr/include/ncbi/netpriv.h +usr/include/ncbi/ni_*.h +usr/include/ncbi/obj*.h +usr/include/ncbi/parsegb.h +usr/include/ncbi/pdiagnos.h +usr/include/ncbi/pgppop.h +usr/include/ncbi/pmfapi.h +usr/include/ncbi/pobutil.h +usr/include/ncbi/posit.h +usr/include/ncbi/profiles.h +usr/include/ncbi/prtutil.h +usr/include/ncbi/prunebsc.h +usr/include/ncbi/puberr.h +usr/include/ncbi/qblastapi.h +usr/include/ncbi/readdb.h +usr/include/ncbi/regex.h +usr/include/ncbi/rpsutil.h +usr/include/ncbi/salign.h +usr/include/ncbi/salmedia.h +usr/include/ncbi/salpacc.h +usr/include/ncbi/salpedit.h +usr/include/ncbi/salprop.h +usr/include/ncbi/salpstat.h +usr/include/ncbi/salptool.h +usr/include/ncbi/salsa.h +usr/include/ncbi/salsap.h +usr/include/ncbi/salstruc.h +usr/include/ncbi/salutil.h +usr/include/ncbi/samutil.h +usr/include/ncbi/satutil.h +usr/include/ncbi/scoremat.h +usr/include/ncbi/sec.h +usr/include/ncbi/seed.h +usr/include/ncbi/seg.h +usr/include/ncbi/seqmgr.h +usr/include/ncbi/seqport.h +usr/include/ncbi/seqsplit.h +usr/include/ncbi/sequtil.h +usr/include/ncbi/simple.h +usr/include/ncbi/simutil.h +usr/include/ncbi/spell*.h +usr/include/ncbi/spidey.h +usr/include/ncbi/splutil.h +usr/include/ncbi/sqnutils.h +usr/include/ncbi/strimprt.h +usr/include/ncbi/strucapi.h +usr/include/ncbi/stsutil.h +usr/include/ncbi/subutil.h +usr/include/ncbi/sug*.h +usr/include/ncbi/tax*.h +usr/include/ncbi/terr.h +usr/include/ncbi/tfuns.h +usr/include/ncbi/thrd*.h +usr/include/ncbi/to*.h +usr/include/ncbi/tree.h +usr/include/ncbi/treemgr.h +usr/include/ncbi/tsprintf.h +usr/include/ncbi/tx*.h +usr/include/ncbi/undefwin.h +usr/include/ncbi/urkbias.h +usr/include/ncbi/urkcnsrt.h +usr/include/ncbi/urkdust.h +usr/include/ncbi/urkepi.h +usr/include/ncbi/urkfltr.h +usr/include/ncbi/urkpcc.h +usr/include/ncbi/urkptpf.h +usr/include/ncbi/urksigu.h +usr/include/ncbi/urktree.h +usr/include/ncbi/urkutil.h +usr/include/ncbi/urlquery.h +usr/include/ncbi/util* +usr/include/ncbi/valid*.h +usr/include/ncbi/vast*.h +usr/include/ncbi/vecsc*.h +usr/include/ncbi/viewmgr.h +usr/include/ncbi/xmlblast.h +usr/lib/libblast*.a +usr/lib/libblast*.so +usr/lib/libncbi*acc.a +usr/lib/libncbi*acc.so +usr/lib/libncbi.a +usr/lib/libncbi.so +usr/lib/libncbicdr.a +usr/lib/libncbicdr.so +usr/lib/libncbiid1.a +usr/lib/libncbiid1.so +usr/lib/libncbimla.a +usr/lib/libncbimla.so +usr/lib/libncbimmdb.a +usr/lib/libncbimmdb.so +usr/lib/libncbiobj.a +usr/lib/libncbiobj.so +usr/lib/libncbitool.a +usr/lib/libncbitool.so +usr/lib/libncbitxc2.a +usr/lib/libncbitxc2.so +usr/lib/libnet*.a +usr/lib/libnet*.so +usr/lib/ncbithr.o --- ncbi-tools6-6.1.20070822.orig/debian/Cn3D-3.0.desktop.in +++ ncbi-tools6-6.1.20070822/debian/Cn3D-3.0.desktop.in @@ -0,0 +1,3 @@ +Name=Cn3D NCBI Database Viewer +GenericName=Database Viewer +Comment=View NCBI databases in 3D --- ncbi-tools6-6.1.20070822.orig/debian/changelog +++ ncbi-tools6-6.1.20070822/debian/changelog @@ -0,0 +1,716 @@ +ncbi-tools6 (6.1.20070822-2) unstable; urgency=low + + * debian/control: set Homepage. + * debian/{control,makemenu,rules,*.desktop.in}: supply XDG desktop + entries and icons for inherently graphical apps. (Closes: #448031.) + * debian/{man.unused,old-blast-man,shlibs.local}: remove (obsolete + cruft; shlibs.local contained only comments anyway.) + + -- Aaron M. Ucko Fri, 26 Oct 2007 19:27:01 -0400 + +ncbi-tools6 (6.1.20070822-1) unstable; urgency=low + + * New upstream release. + * vibrant/vib{main,wndws.c}: restore sane behavior in key corner cases + (no Nlm_Main, no DISPLAY). + * debian/{control,rules}: ncbilogo.ico now contains multiple variants; + use icotool from icoutils to extract the right one to convert. + * debian/libncbi6-dev.install: handle two new "unclaimed" headers. + * debian/ncbi-tools-bin.install: drop getfeat (dead), entrcmd (obsolete). + * debian/ncbi-tools-x11.install: drop netentcf (dead), Nentrez (obsolete). + * debian/ncbi-tools-x11.links: repoint entrez at entrez2 (vs. Nentrez). + * debian/rules: stop building Nentrez; update list of built but unwanted + executables. + * debian/makemenu: fix section assignments per menu policy 2.1.35. + * Update man pages. + + -- Aaron M. Ucko Mon, 08 Oct 2007 16:42:46 -0400 + +ncbi-tools6 (6.1.20061015-2) unstable; urgency=low + + * debian/installman: don't append .gz to *.htm(l) files' paths, as + dh_compress (rightly) excludes them by default. (Closes: #412651.) + * debian/makemenu: correct vibrate's package requirement to libvibrant6a + (closes: #429955, #429956); generate appropriate linda overrides (for + command-not-exist), another "problem" with the setup. + * debian/libvibrant6a.override (new): suppress lintian warnings about + the package name not precisely matching any SONAME. + + -- Aaron M. Ucko Fri, 29 Jun 2007 13:29:17 -0400 + +ncbi-tools6 (6.1.20061015-1) unstable; urgency=low + + * New upstream release. + * Don't bother linking against indirectly used system libraries. + * Update man pages. + + -- Aaron M. Ucko Sun, 22 Oct 2006 19:32:02 -0400 + +ncbi-tools6 (6.1.20060507-3) unstable; urgency=low + + * Drop transitional packages, which are now entirely redundant thanks to + the binNMU of clustalx for i386 earlier this June. (Closes: #322059.) + * Migrate to lesstif2, renaming libvibrant6(-dbg) to libvibrant6a(-dbg) + to avoid any possibility of version skew. [Lesstif lacks versioned + symbols, though admittedly so does Vibrant.] (Closes: #374233.) + * Make debian/stamp-setup a dependency of common-configure-indep as well + as common-configure-arch so that building via an immediate call to + "fakeroot debian/rules binary" works properly, per #373971. + * Explicitly build depend on modular versions of *all* relevant X + libraries, per the other issue in #373971 (and to ensure that the arm + autobuilder's failure mode *really* can't recur). + + -- Aaron M. Ucko Sat, 24 Jun 2006 09:28:43 -0400 + +ncbi-tools6 (6.1.20060507-2) unstable; urgency=low + + * Version the build-dependency on libxmu-dev to (>= 1:1) to ensure that + we *can* actually drop -I/usr/X11R6/include and -L/usr/X11R6/lib, + avoiding the failure mode observed on the arm autobuilder. + * Further increase cdbs's minimum required version to the brand new + 0.4.40, which automatically sets DEB_DBG_PACKAGE_* appropriately. + + -- Aaron M. Ucko Mon, 29 May 2006 20:42:28 -0400 + +ncbi-tools6 (6.1.20060507-1) unstable; urgency=low + + * New upstream release (issued on May 26, but from older sources). + * Drop obsolete -I/usr/X11R6/include and -L/usr/X11R6/lib flags. + * Rework inter-package relationships with the help of dpkg-dev 1.13.19. + * Migrate remaining shared library support files (including vibrate) to + ncbi-data, as they're conveniently all architecture-independent. + * Add cleanasn (new) to the list of applications to build, and give it a + man page. + * Update existing man pages. + * Increase the cdbs requirement to 0.4.39-0.1, and drop workarounds for + (some?) older versions. + * Switch to debhelper compatibility level 5, with its reworked -dbg + package handling. + * Standards-Version: 3.7.2. + + -- Aaron M. Ucko Mon, 29 May 2006 16:50:27 -0400 + +ncbi-tools6 (6.1.20060301-1) unstable; urgency=low + + * New (relatively, anyway ;-P) upstream release. + * (Build-)depend directly on libgl(u)1-mesa-dev by default (but keep + the alternate [build-]dependencies on virtual packages, of course). + * Add insdseqget to the list of applications to build. + * Stop installing wwwblast.h, which is private to code we don't even + build. + * Update man pages (and add one for insdseqget, forked from gbseqget's). + + -- Aaron M. Ucko Sun, 16 Apr 2006 12:52:44 -0400 + +ncbi-tools6 (6.1.20051206-1) unstable; urgency=low + + * New upstream release. + * Temporarily switch to pmake (added to Build-Depends) for upstream's + makefiles, as GNU make 3.81.b4 gets mysteriously confused when trying + to build from them (but, oddly, only when invoked from debian/rules). + * Add "new" blastall_old executable to the blast2 package. + * Reshuffle documents slightly, and make sure to register all top-level + HTML documents with doc-base. + * Loosen libncbi6's dependency on ncbi-data to accommodate binary-only + NMUs. + + -- Aaron M. Ucko Thu, 12 Jan 2006 18:50:27 -0500 + +ncbi-tools6 (6.1.20050828-1) unstable; urgency=low + + * New upstream release + - Adds two new programs: sbtedit (in ncbi-tools-x11) and trna2sap + (in ncbi-tools-bin). + * Drop obsolete alternative (build-)dependencies on ancient versions of + xlibs-dev, and silly build-dependency on libglu1-xorg | libglu1c2, and + resync libvibrant-dev's dependencies properly. + * Add man pages for the new programs, and clean up and update others as + needed. + + -- Aaron M. Ucko Fri, 4 Nov 2005 16:41:18 -0500 + +ncbi-tools6 (6.1.20050605-2) unstable; urgency=low + + * Adjust default libglu-dev to libglu1-xorg-dev to avoid confusing the + autobuilders. + + -- Aaron M. Ucko Fri, 15 Jul 2005 23:37:06 -0400 + +ncbi-tools6 (6.1.20050605-1) unstable; urgency=low + + * New upstream release. + * Enable asn2asn via VIB rather than unnecessarily modifying + makedemo.unx, and add (and document) nps2gps and trna2tbl along + the way. + * Make sure to build with libglu1c2 for the C++ transition. + * Don't set DEB_DH_SHLIBDEPS_ARGS; it's not necessary with current + versions of dpkg and cdbs, and -L isn't actually additive anyway. + * Bump standards-version to 3.6.2 (no changes needed). + + -- Aaron M. Ucko Fri, 15 Jul 2005 19:03:40 -0400 + +ncbi-tools6 (6.1.20050429-1) unstable; urgency=low + + * New upstream release. + * Add and document asn2all, asn2fsa, asnval, and gene2xml, even though + makedis.csh still omits them. + * Make Nentrez and Psequin available under the saner names entrez and + sequin. + * Tweak debian/rules to better handle "draft" builds from subversion. + + -- Aaron M. Ucko Tue, 17 May 2005 17:43:14 -0400 + +ncbi-tools6 (6.1.20041020-3) unstable; urgency=low + + * Fix FTBFS under GCC 4.0 caused by inconsistent use of "static" on + functions. (Closes: #295110.) + * Add a watch file, now that we can. (Upstream's layout needs version=3.) + + -- Aaron M. Ucko Sun, 27 Mar 2005 12:00:15 -0500 + +ncbi-tools6 (6.1.20041020-2) unstable; urgency=low + + * Add spidey to ncbi-tools-bin by Steffen Moeller's request, and + incorporate some documentation he supplied for it. (Closes: #291895.) + + -- Aaron M. Ucko Tue, 25 Jan 2005 18:16:49 -0500 + +ncbi-tools6 (6.1.20041020-1) unstable; urgency=low + + * New upstream release; debian/* resynched as necessary. + - Fixes Vibrant invisible text bug! + * Take advantage of menu 2.1.8's support for multiple required packages. + + -- Aaron M. Ucko Mon, 1 Nov 2004 20:07:56 -0500 + +ncbi-tools6 (6.1.20040616-1) unstable; urgency=low + + * New upstream release. + * debian/blast2.docs: adjusted for new arrangement (a separate + source-tree directory full of HTML files). + * debian/{control,lib*-dbg.install,rules}: switch to new-style -dbg + packages containing just the stripped-out symbols. + * debian/{installman,ncbi-tools-bin.install,rules}: upstream has dropped + f(asta)merge. + + -- Aaron M. Ucko Sat, 26 Jun 2004 00:18:09 -0400 + +ncbi-tools6 (6.1.20040505-1) unstable; urgency=low + + * New upstream release. + * debian/rules: + - set BLAST_VERSION from demo/.BLAST_VERSION rather than parsing + tools/blastdef.h. + + -- Aaron M. Ucko Sat, 15 May 2004 17:49:45 -0400 + +ncbi-tools6 (6.1.20040204-3) unstable; urgency=low + + * Update X-related (build-)dependencies per the changes in 4.3. + * Reunite the Vibrant packages, with libvibrant.so.6 and + libncbicn3d.so.6 always pointing at the OpenGL-enabled versions, now + that xlibmesa-gl merely suggests the heavyweight packages containing + acceleration modules. + * As such, tighten shlibdeps for libvibrant6 to avoid possible trouble. + + -- Aaron M. Ucko Wed, 10 Mar 2004 18:48:26 -0500 + +ncbi-tools6 (6.1.20040204-2) unstable; urgency=low + + * debian/{libncbi6-dev,rules}: account for new include subdirectories. + + -- Aaron M. Ucko Sun, 8 Feb 2004 22:42:12 -0500 + +ncbi-tools6 (6.1.20040204-1) unstable; urgency=low + + * New upstream release. + * debian/copyright: expand public domain notice to full length. + * debian/*.install: install newly added files. + * debian/rules: + - supply appropriate -L args to dh_shlibdeps (accidentally lost when + converting to CDBS). + - various minor cleanups. + * demo/debruijn.c: fix fencepost error. + * desktop/bspview.c, vibrant/netscape.c: launch sensible-browser rather + than netscape. + * doc/man/blast.1: document new blast2 executable. + * doc/man/debruijn.1: new, based on help output. + * make/makeshlb.unx: add dependency info for libblast(api). + + -- Aaron M. Ucko Fri, 6 Feb 2004 22:03:25 -0500 + +ncbi-tools6 (6.1.20031028-1) unstable; urgency=low + + * New upstream release. + * debian/blast2.docs: follow README.* -> *.txt renaming. + * debian/libncbi6-dev.install: add new headers scoremat.h and wwwblast.h. + * debian/installman: new; factored out of debian/rules, and enhanced + to look in doc/man before debian/man and tweak pages as needed. + * debian/instdoc: removed (not used since conversion to CDBS). + * debian/man/*: remove pages now committed upstream. + * debian/{ncbi-tools-bin.files,rules}: remove cdscan (obsolete). + * debian/rules: run new debian/installman script. + * debian/vibrant/vibwndws.c: add a weak declaration of Nlm_Main + (and code to complain if it's not satisfied) here too. + + -- Aaron M. Ucko Mon, 10 Nov 2003 22:51:03 -0500 + +ncbi-tools6 (6.1.20030421-6) unstable; urgency=low + + * debian/control: Fix libncbi6-dbg to depend directly on libncbi6 + rather than on the transitional ncbi-tools6 package. + * debian/{control,lib*-dbg.install,rules}: While I'm at it, move + unstripped libraries from /usr/lib/ncbi-tools-dbg to /usr/lib/debug. + + -- Aaron M. Ucko Fri, 17 Oct 2003 23:24:32 -0400 + +ncbi-tools6 (6.1.20030421-5) unstable; urgency=low + + * debian/control: + - Downgrade oldlibs packages (ncbi-tools6 and vibrant6) to priority + extra, per override. + - Bump CDBS build-dependency to >= 0.4.12. + - Drop redundant entries from build-depends-indep. + * debian/libncbi6.doc-base: Actually supply the documentation + directory's current name. (Closes: #215398.) + * debian/rules: Take advantage of CDBS 0.4.12's support for -dbg packages. + * corelib/ncbimain.c: Use an __attribute__((weak)) declaration for + Nlm_Main rather than a dummy implementation + #pragma weak. + * vibrant/shim3d.c: Likewise for Cn3D_GetCurrentOGLData. + + -- Aaron M. Ucko Sun, 12 Oct 2003 11:18:21 -0400 + +ncbi-tools6 (6.1.20030421-4) unstable; urgency=low + + * debian/rules: compile with -mieee on Alpha to fix platform-specific + FPEs. (Closes: #127224). + * doc/README.bls: updated to latest upstream version (which includes the + missing release notes for 2.2.6). + + -- Aaron M. Ucko Tue, 2 Sep 2003 11:13:09 -0400 + +ncbi-tools6 (6.1.20030421-3) unstable; urgency=low + + * debian/control: + - Bump Standards-Version to 3.6.1 (no changes needed). + - blast2, ncbi-tools-bin: Suggest libvibrant6 rather than vibrant6. + - libvibrant6-gl{,-dev}, ncbi-tools-x11: lower priority to extra due + to conflicts with libvibrant6-nogl, which is optional. + + -- Aaron M. Ucko Fri, 22 Aug 2003 20:21:56 -0400 + +ncbi-tools6 (6.1.20030421-2) unstable; urgency=low + + * The "overdue cleanup" release. + * general (debian/*, make/makeshlb.unx): + - Rename library packages to start with "lib"; ncbi-tools6 and vibrant6 + are now dummy forwarding packages. + - Move libvibgif.so.6 to libncbi6, since it's independent of X. + - Split GL and non-GL variants of libvibrant and libncbicn3d into + separate packages. + - Standardize on the network version of the Entrez 1 access library + (libncbiNacc), if only for the sake of other libraries that need any + of the three variants; the CDROM-only version's not so useful + nowadays, and the combo version seems to misfire without the CDs. + Note that all three remain available in static form. + - Handle the circular relationship between libncbiNacc and libnetentr by + linking the PIC version of libnetentr.a into libncbiNacc.so and making + libnetentr.so.6 merely another link to libncbiNacc.so.6. (Kludge.) + - Set up proper shared library dependencies, now that it is possible to + do so uniquely. + - Now compliant with Policy 3.6.0. + * connect/ncbi_http_connector.c: Don't half-close sockets after sending + headers, as we can't always successfully read from them afterwards + (due to broken firewalls?). + * debian/rules: + - Switch to CDBS, despite upstream's funky build system. + - Stop imposing the obsolete menu icon color restriction. + + -- Aaron M. Ucko Mon, 28 Jul 2003 20:11:26 -0400 + +ncbi-tools6 (6.1.20030421-1) unstable; urgency=low + + * New upstream release. + * api/aliread.c: avoid char vs. EOF comparisons. + * debian/{blast2,ncbi-tools6-dev}.docs: package new upstream docs. + * debian/control: + - Change section to devel. + - Bump standards version to 3.5.9 (already compliant). + - Change preferred libpng-dev to libpng12-dev (12-0-dev went away). + * debian/man/Psequin.1: sequin seems to take options after all; + (very roughly) document them. + * debian/man/{asn2gb,blast,fastacmd,gbseqget,gil2bin,tbl2asn}.1: + - Update to reflect current help output. + * debian/rules: add bl2seq to VIB so we still actually build it. + * demo/gil2bin.c: #include for GetGisFromFile prototype. + + -- Aaron M. Ucko Sun, 27 Apr 2003 12:41:48 -0400 + +ncbi-tools6 (6.1.20021213-5) unstable; urgency=low + + * debian/control: Build-Conflict on xlibmesa-glu-dev (<< 4.2.1-6), and + drop corresponding workarounds. (See #178310 and #178374.) + + -- Aaron M. Ucko Tue, 25 Feb 2003 23:44:39 -0500 + +ncbi-tools6 (6.1.20021213-4) unstable; urgency=low + + * Oops, add a dependency on xlibmesa-gl-dev|libgl-dev because + xlibmesa-glu-dev doesn't seem to depend on it.... + * Likewise for xlibmesa3-glu | libglu1, due to #178310. + * Still no (intentional) changes in actual content relative to + 6.1.20021213-2. + + -- Aaron M. Ucko Fri, 24 Jan 2003 22:07:51 -0500 + +ncbi-tools6 (6.1.20021213-3) unstable; urgency=low + + * Update OpenGL deps to xlibmesa-glu-dev|libglu-dev. + * Hack debian/rules to give blast2 a more meaningful version number. + * Finally rename *.files to *.install and change dh_movefiles -a to + dh_install -a --autodest --list-missing --sourcedir=debian/tmp. (Drop + ncbi-data.files in favor of installing directly into debian/ncbi-data.) + * Add lintian overrides for menu-icon-missing warnings. + + -- Aaron M. Ucko Fri, 24 Jan 2003 14:43:59 -0500 + +ncbi-tools6 (6.1.20021213-2) unstable; urgency=low + + * Address char-signedness issues. (Closes: #177392) + + -- Aaron M. Ucko Tue, 21 Jan 2003 21:04:50 -0500 + +ncbi-tools6 (6.1.20021213-1) unstable; urgency=low + + * New upstream release. (Man pages updated.) + * Change preferred libpng-dev to libpng12-0-dev rather than libpng3-dev + (which is a dummy package these days). + * Abandon plans for switching to lesstif2, as Vibrant seems to work + better with lesstif1. + + -- Aaron M. Ucko Tue, 17 Dec 2002 22:34:26 -0500 + +ncbi-tools6 (6.1.20021119-1) unstable; urgency=low + + * New upstream release. (Man pages updated accordingly.) + * Update for policy 3.5.8: move menu entries to Apps/Science per #162812. + * Indicate options in man pages with \- rather than - per #159872. + * Move icons from /usr/X11R6/include/X11/pixmaps to /usr/share/pixmaps. + + -- Aaron M. Ucko Thu, 21 Nov 2002 09:05:38 -0500 + +ncbi-tools6 (6.1.20020828-2) unstable; urgency=low + + * Try to use madvise only if MADV_NORMAL is actually defined. + + -- Aaron M. Ucko Thu, 5 Sep 2002 10:49:01 -0400 + +ncbi-tools6 (6.1.20020828-1) unstable; urgency=low + + * New upstream release. + * Update man pages based on current help output. + * Go to standards version 3.5.7 (support "noopt" rather than "debug" in + DEB_BUILD_OPTIONS). + * Strictly speaking, the ABI changes should necessitate a new soname, + but no external Debian packages seem to use the affected interfaces, + so I'll be lazy. You may need to rebuild any local binaries you have. + (Conflict with old versions of our binary packages, though.) + + -- Aaron M. Ucko Wed, 4 Sep 2002 20:30:31 -0400 + +ncbi-tools6 (6.1.20020426-5) unstable; urgency=low + + * Add a second hyphen before (no-)whole-archive to fix the ARM build. + + -- Aaron M. Ucko Mon, 26 Aug 2002 18:41:08 -0400 + +ncbi-tools6 (6.1.20020426-4) unstable; urgency=low + + * Partially migrate to debhelper v4. + * Pave the way for C++ toolkit packages (in progress): + - Provide a weak default definition of Nlm_Main so that our shared + libncbi doesn't bite applications which supply their own main(). + - Rename Cn3D to Cn3D-3.0 and register it as an alternative for Cn3D. + * Move to libpng3 (only affects applications). + * Rename fmerge to fastamerge to resolve conflict with fhist. + (Closes: #155791) + + -- Aaron M. Ucko Fri, 23 Aug 2002 22:34:17 -0400 + +ncbi-tools6 (6.1.20020426-3) unstable; urgency=low + + * Remove getseq (which isn't terribly useful) to resolve conflict with + hmmer. (Closes: #147793) + + -- Aaron M. Ucko Thu, 23 May 2002 21:20:47 -0400 + +ncbi-tools6 (6.1.20020426-2) unstable; urgency=low + + * Enable large-file support; please let me know if this turns out to + break anything. (Closes: #144531) + * Don't build ncbithr.o or link against -lpthread unless that library + actually exists; should help on non-Linux ports. + + -- Aaron M. Ucko Thu, 9 May 2002 19:26:35 -0400 + +ncbi-tools6 (6.1.20020426-1) unstable; urgency=low + + * New upstream release; apparently fixes formatdb segfault on PowerPC + (closes: #144783). + * Some existing interfaces have changed, but not enough to justify + bumping the soname; if binaries built against older revisions of the + toolkit no longer work, try rebuilding them. (I don't believe this + affects any other Debian packages.) + * Updated man pages based on current help output. + * Patched both versions (regular and Vibrant) of common argument- + processing code to honor "--help" (closes: #144785). + + -- Aaron M. Ucko Sun, 28 Apr 2002 18:30:43 -0400 + +ncbi-tools6 (6.1.20011220a-2) unstable; urgency=low + + * Whoops, ncbi-data should replace pre-split versions of ncbi-tools6. + + -- Aaron M. Ucko Thu, 4 Apr 2002 22:13:09 -0500 + +ncbi-tools6 (6.1.20011220a-1) unstable; urgency=low + + * New upstream release, mostly appears to address some megablast issues. + * Deal with some 64-bit-cleanliness issues. + * Partially fix Cn3D lossage in #127224. (It still crashes, but later.) + * Fix copymat lossage with trailing spaces and improve its error + messages (closes: #138933). + * Split architecture-independent files into new ncbi-data package. + * Fix path to libXm.so.1 in vibrate. + + -- Aaron M. Ucko Sun, 31 Mar 2002 10:33:49 -0500 + +ncbi-tools6 (6.1.20011220-2) unstable; urgency=low + + * Update manpages based on current help output. + * Fix typo in description (ASN1 -> ASN.1). + * Use $(CC) rather than gcc in makeshlb.unx. + * Build asn2asn. + + -- Aaron M. Ucko Fri, 28 Dec 2001 13:48:20 -0500 + +ncbi-tools6 (6.1.20011220-1) unstable; urgency=low + + * New upstream release (Closes: #126625). + * Bug #31724 is probably fixed by now, and too vague to do much of + anything with anyway. (Closes: #31724; please supply useful details + if reopening.) + * Tweak rules so that the shlibs dependency is always + (>= [latest.upstream.version]-1). + + -- Aaron M. Ucko Thu, 27 Dec 2001 21:08:17 -0500 + +ncbi-tools6 (6.1.20010709-9) unstable; urgency=low + + * Menu seems to be broken on some architectures, so drop build + dependency and add a copy of cmap.xpm to debian/. + * Slightly rework treatment of icons in debian/rules. + * Change "c-shell" to "tcsh|c-shell" in build-deps to address buildd + warnings. + * Add lintian overrides for new menu file. + + -- Aaron M. Ucko Thu, 20 Dec 2001 11:47:53 -0500 + +ncbi-tools6 (6.1.20010709-8) unstable; urgency=low + + * Change priority of debugging libraries to extra, per the override file. + * Add menu file for ncbi-tools6-dev (asntool) and menu icons. + * Add build-depends on ImageMagick and menu for icon creation. + * Clean up internal script for creating menu files. + + -- Aaron M. Ucko Tue, 18 Dec 2001 21:12:41 -0500 + +ncbi-tools6 (6.1.20010709-7) unstable; urgency=low + + * Change section of debugging libraries from libs to devel. + + -- Aaron M. Ucko Sun, 18 Nov 2001 20:36:31 -0500 + +ncbi-tools6 (6.1.20010709-6) unstable; urgency=low + + * Introduce debugging libraries. (Closes: #38354). + + -- Aaron M. Ucko Mon, 12 Nov 2001 12:08:44 -0500 + +ncbi-tools6 (6.1.20010709-5) unstable; urgency=low + + * Sigh, the change in -4 intended to fix arm broke it instead; revert to + __arm__. Where'd I put that paper bag? ;-) + * Allow #cpu(...) and #machine(...) for all platforms. + * Downgrade "unknown platform" to a warning; the code mostly doesn't + care which PROC_XXX macro, if any, gets defined (and when it does, may + read too much from it; see below). + * Fix uses of PROC_XXX not to assume that MIPS -> IRIX or HPPA -> HP/UX. + * Use appropriate sysconf to get processor count. + + -- Aaron M. Ucko Tue, 16 Oct 2001 13:26:49 -0400 + +ncbi-tools6 (6.1.20010709-4) unstable; urgency=low + + * Also fix test for m68k. Why can't the macros be more consistent? + * Check everything else against the GCC sources and find that __arm__ + should be arm. + * That should be all of these; apologies for the inconvenience. + + -- Aaron M. Ucko Sat, 13 Oct 2001 14:50:03 -0400 + +ncbi-tools6 (6.1.20010709-3) unstable; urgency=low + + * Fix test for powerpc in ncbilcl.lnx. (Check for two likely + definitions to be extra safe. ;-)) + + -- Aaron M. Ucko Fri, 12 Oct 2001 10:50:39 -0400 + +ncbi-tools6 (6.1.20010709-2) unstable; urgency=low + + * Fix problems caught by autobuilders: + * Rewrite clean rule to avoid mkdir. (Closes: #115103) + * Add build-dependency on c-shell (ugh) for ln-if-absent. + * + * Whoops, my previous sweep missed two (old, minor) bugs on + ncbi-tools6-dev: + * 31724: I suspect I can close this by now, but don't have a whole lot + of information to go on; could somebody on an Alpha investigate? + * 38354: Debugging libraries would be a good idea, but I'm holding off + until autobuilds succeed because adding more binary packages + introduces ftpmaster wait. + * + * Keep shlib requirement at >= 6.1.20010709-1, because this version + doesn't change anything relevant. + * Add HTTP URL for HTML SDK docs. + * Optimize out blast.REAL build. + + -- Aaron M. Ucko Wed, 10 Oct 2001 18:42:44 -0400 + +ncbi-tools6 (6.1.20010709-1) unstable; urgency=low + + * New upstream version; adds more apps, and includes newer BLAST (2.2.1 + rather than 2.0.9). (Closes: #33451, #37966, #37967, #47369, #101168) + * Repackaged largely from scratch, acknowledging the convoluted nature + of the upstream build system. + * Put ncbi-tools6 and vibrant6 in section "libs", where they belong, + rather than "devel" (already correct in override file). + * Used the same form of my name in the control file and the changelog so + that katie doesn't think I'm making NMUs. + * Acknowledged my own last "NMU" (Closes: #100247, #103550, #104365) + * Enabled thread support for appropriate applications. (Closes: #35216) + * Added automatic fallback to /etc/ncbi if NCBI not set in the + environment; did away with no-longer-necessary wrappers. + * New binary packages for apps: ncbi-tools-bin and ncbi-tools-x11. + * Moved data to /usr/share/ncbi/data, since it's architecture-independent. + * Closes all existing bugs. Let's see how long that lasts... + and no fair filing silly reports just to thwart me. ;-) + * Dropped text version of old SDK docs in favor of pointer to online HTML + version. + * Don't link against Vibrant unnecessarily; instead, provide a wrapper + script (vibrate) with the same net effect. + * Added menu entries (using vibrate for apps it benefits). + * Added Lintian overrides to deal with cross-package menu entries. + * Registered with doc-base. + * Clean by Lintian 1.20.15, modulo the aforementioned overrides. + + -- Aaron M. Ucko Sat, 6 Oct 2001 10:51:36 -0400 + +ncbi-tools6 (6.0.2-3) unstable; urgency=low + + * Adopted. (Closes: #100247) + * Acknowledge previous NMUs. (Closes: #103550, #104365) + * Stop installing /usr/share/doc/ncbi-tools6/NCBI/fa2htgs/updateHtgsDoc; + it was causing a Lintian error (executable file under /usr/share/doc) + and not useful as-is anyway (referring to paths only valid on NCBI + systems). + * Honor DEB_BUILD_OPTIONS, and build without -g by default. + * Above change should suffice to bump standards version to 3.5.6. Yay! + * Now clean by Lintian 1.20.14.1. + + -- Aaron M. Ucko Thu, 6 Sep 2001 11:05:49 -0400 + +ncbi-tools6 (6.0.2-2.2) unstable; urgency=low + + * NMU + * The previous maintainer has resigned. Setting maintainer to Debian QA + Group . + * debian/ncbi-tools6-dev.README.debian: add final newline to shut diff up + * debian/control: tidied up package descriptions + * debian/rules: use dh_shlibdeps -l instead of LD_LIBRARY_PATH + * debian/{shlibs,vibrant6.shlibs}: while we're at it, why don't we have + some shlibs files to go with these shared library packages, like they + taught us in freshman year at Debian University + * Thanks to the above two fixes... (Closes: #104365) + + -- Dr. Branden Robinson Sat, 11 Aug 2001 20:57:17 -0500 + +ncbi-tools6 (6.0.2-2.1) unstable; urgency=low + + * Non-maintainer upload. + * va_arg promotes shorts to ints. This is flagged as an error by + gcc >= 2.96. Closes: #103550 + + -- LaMont Jones Mon, 9 Jul 2001 21:39:34 -0600 + +ncbi-tools6 (6.0.2-2) unstable; urgency=low + + * Adopted by new maintainer; closes: #92794, #92796, #92798, #48176 + * Corrected typo in manpage for formatdb; closes: #38483 + * Removed self-conflict of vibrant-dev; closes: #49712 + * Changed the double installation of the copyright file by ncbi-tools6 and + ncbi-tools6-dev into the same doc directory (and added a README.Debian in + /usr/share/doc/ncbi-tools6-dev); closes: #51122, #77541, #56643 + * Added the installation of README.blast. + * Updated to newer standards version and added Build-Depends. + * Added debhelper token to vibrant6.preinst to fix lintian warning. + * Moved blast2 from section misc to science, because it is a tool that + is exclusively useful for molecular biologists. + + -- Dr. Guenter Bechly Fri, 13 Apr 2001 15:12:10 +0200 + +ncbi-tools6 (6.0.2-1.1) unstable; urgency=low + + * NMU. + * Recompiled against lesstif1. Closes: #48176 + + -- Adam Heath Mon, 25 Oct 1999 07:05:49 -0500 + +ncbi-tools6 (6.0.2-1) unstable; urgency=low + + * New upstream release (includes Blast 2.0.8). + Addresses #33451 but does not solve it completely. + * Manual page. Closes #30227 + * Add the vibrant package + * Proper symlinks in -dev packages. Closes #31619 + + -- Stephane Bortzmeyer Mon, 15 Feb 1999 12:55:01 +0100 + +ncbi-tools6 (6.0.1-1) unstable; urgency=low + + * New upstream release + * Add the blast package + + -- Stephane Bortzmeyer Thu, 12 Nov 1998 15:55:02 +0100 + +ncbi-tools6 (6.0-3) frozen; urgency=low + + * Changes in the dependencies in control. Closes #28610 + * Change in rules: the source package was broken and uncompilable. Closes #28978 + + -- Stephane Bortzmeyer Wed, 28 Oct 1998 09:16:49 +0100 + +ncbi-tools6 (6.0-2) unstable; urgency=low + + * Various lintian warnings suppressed + * Not all files are copied in /usr/lib/ncbi/data, to save space + + -- Stephane Bortzmeyer Mon, 26 Oct 1998 15:59:25 +0100 + +ncbi-tools6 (6.0-1) unstable; urgency=low + + * Initial Release. First public release. + + -- Stephane Bortzmeyer Tue, 22 Sep 1998 17:23:12 +0200 + + --- ncbi-tools6-6.1.20070822.orig/debian/.ncbirc +++ ncbi-tools6-6.1.20070822/debian/.ncbirc @@ -0,0 +1,74 @@ +[LINKS] +CHANNELS=LINKS_FROM_MEDLINE, LINKS_FROM_SEQUENCE + +[SEQUENCE_CD_DESC] +MEDIA=ENTREZ_SEQ_CD + +[REFERENCE_FROM_NET] +MEDIA=ENTREZ_NET + +[SEQUENCE_FROM_NET] +MEDIA=ENTREZ_NET + +[LINKS_FROM_NET] +MEDIA=ENTREZ_NET +ENTR_SEQ__ENTR_SEQ=1 +ENTR_SEQ__ENTR_REF=1 +ENTR_REF__ENTR_SEQ=1 +ENTR_REF__ENTR_REF=1 + +[NCBI] +DATA=/usr/share/ncbi/data/ +MEDIA=ENTREZ_NET +AsnLoad= + +[ENTR_LINK] +CHANNELS=LINKS_FROM_NET + +[ENTR_REF] +CHANNELS=REFERENCE_FROM_NET + +[ENTR_SEQ] +CHANNELS=SEQUENCE_FROM_NET + +[ENTREZ] +SERVICES=ENTR_LINK, ENTR_REF, ENTR_SEQ + +[ENTREZ_NET] +TYPE=NET +SERVICE_NAME=Entrez +RESOURCE_NAME=Entrez +RESOURCE_TYPE=Entrez +SERV_VERS_MIN=1 +SERV_VERS_MAX=0 +RES_VERS_MIN=150 +RES_VERS_MAX=0 +FORMAL_NAME=Entrez Network Service + +[NET_SERV] +DISPATCHER=130.14.25.211 +DISP_ALT_1=dispatch1.nlm.nih.gov +DISP_ALT_2=130.14.25.47 +DISP_ALT_3=dispatch2.nlm.nih.gov +DISP_ALT_4=dispatch3.nlm.nih.gov +DISP_ALT_5=130.14.25.1 +DISPSERIALNO=6 +DISP_USERNAME=letondal +DISP_RECONN_ACTION=CONT + +[FONTS] +JOURNAL=Helvetica,12,i +VOLUME=Helvetica,12,b +PAGES=Helvetica,12 +TITLE=Times,18,b +AUTHORS=Times,18 +AFFILIATION=Times,14 +ABSTRACT=Times,14 +MESH=Times,12 +HEADING=Helvetica,14,b +REFERENCE=Helvetica,12 +SEQUENCE=Courier,12 +STANDARD=Times,12 +DISPLAY=Courier,10 +FETCHED=Times,14 + --- ncbi-tools6-6.1.20070822.orig/debian/libvibrant6-dev.postinst +++ ncbi-tools6-6.1.20070822/debian/libvibrant6-dev.postinst @@ -0,0 +1,13 @@ +#!/bin/sh +set -e + +# Formerly used to support libvibrant6-gl-dev's shenanigans. (Don't ask.) +olddir=/usr/lib/libvibrant-nogl + +if [ "$1" = configure ] && [ -d $olddir ]; then + echo "Cleaning up obsolete directory $olddir ..." + rm -f $olddir/libncbicn3d.so.6 $olddir/libvibrant.so.6 + rmdir --ignore-fail-on-non-empty $olddir +fi + +#DEBHELPER# --- ncbi-tools6-6.1.20070822.orig/debian/ddv.desktop.in +++ ncbi-tools6-6.1.20070822/debian/ddv.desktop.in @@ -0,0 +1,3 @@ +Name=DDV Sequence Alignment Viewer +GenericName=Sequence Alignment Viewer +Comment=View multiple sequence alignment for GenBank --- ncbi-tools6-6.1.20070822.orig/debian/makemenu +++ ncbi-tools6-6.1.20070822/debian/makemenu @@ -0,0 +1,70 @@ +#!/bin/sh +if [ "x$1" = "x-v" ]; then + vibrate=true + shift +else + vibrate=false +fi +package=`basename $1 .install` +if [ $vibrate = true ]; then + linda_dir=debian/$package/usr/share/linda/overrides + mkdir -p $linda_dir + echo 'Tag: command-not-exist' > $linda_dir/$package + packages="libvibrant6a,$package" +else + packages=$package +fi +menu=`echo $1 | sed -e 's/install$/menu/'` +while read command junk; do + case $command in + */bin/*) ;; + * ) continue ;; + esac + case $package in + libncbi6-dev) section="Applications/Programming" ;; + * ) section="Applications/Science/Biology" ;; + esac + case $command in + # Doesn't use requisite argument-handling framework + */ncbisort) continue ;; + */Nentrez ) title=Entrez ;; + */Psequin ) title=Sequin ;; + */netentcf) title="Entrez net config" ;; + * ) title=`basename $command` ;; + esac + icondir=/usr/share/pixmaps + case $command in + */asntool) icon=$icondir/asntool.xpm ;; + *) icon=$icondir/ncbilogo.xpm ;; + esac + if [ $vibrate = true ]; then + command="usr/bin/vibrate /$command" + else + # generate an XDG .desktop file too + apps=debian/$package/usr/share/applications + base=`basename $command` + if test -f debian/$base.desktop.in; then + mkdir -p $apps + cat >$apps/$base.desktop <> $apps/$base.desktop + cat >>$apps/$base.desktop <&2 + fi + fi + cat < "$menu" + + --- ncbi-tools6-6.1.20070822.orig/debian/installman +++ ncbi-tools6-6.1.20070822/debian/installman @@ -0,0 +1,51 @@ +#!/usr/bin/perl -w +use strict; +use IO::File; + +my $pkg = shift; +my $outdir = "debian/$pkg/usr/share/man/man1"; +my $USD = "/usr/share/doc"; +system("mkdir", "-p", $outdir) && die "Couldn't create $outdir"; + +foreach my $x (@ARGV ? @ARGV : ) { + $x =~ s:.*/::; + my $xin = $x; +# gone as of 6.1.20040616 +# if ($x eq 'fastamerge') { +# $xin = 'fmerge'; # renamed in Debian per #155791 +# } + foreach my $dir qw(doc/man debian/man) { + if (-f "$dir/$xin.1") { + my $in = new IO::File("<$dir/$xin.1") + or die "Couldn't open $dir/$xin.1: $!"; + my $out = new IO::File(">$outdir/$x.1") + or die "Couldn't open $outdir/$x.1: $!"; + while (<$in>) { + # s/fmerge/fastamerge/g; + # s/FMERGE/FASTAMERGE/g; + s:(\w+)/README:README.$1:g; + while (/^(.*)(?; + if (!@matches) { + warn "[$x] $USD/*/$main not found in any package"; + } elsif (@matches > 1) { + warn "[$x] $USD/*/$main found in multiple packages"; + } else { + my $m = $matches[0]; + $m .= '.gz' if ((-s $m) > 4096 && $m !~ /\.html?$/); + $m =~ s:^debian/[^/]*::; + print $out $pre . $m; + } + # Consider just the remaining text next time, + # and make sure it ends with exactly one newline. + chomp $post; + $_ = "$post\n"; + } + print $out $_; + } + last; + } + } + -f "$outdir/$x.1" || warn "Unable to find a man page for $x"; +} --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6-dev.README.debian +++ ncbi-tools6-6.1.20070822/debian/libncbi6-dev.README.debian @@ -0,0 +1,5 @@ +The (outdated) SDK manual also exists in HTML form at +ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/sdkdoc/index.html + +Aaron M. Ucko , Mon Sep 10 10:40:35 EDT 2001 + --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.install +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.install @@ -0,0 +1,6 @@ +usr/bin/Cn3D-3.0 +usr/bin/Psequin +usr/bin/ddv +usr/bin/entrez2 +usr/bin/sbtedit +usr/bin/udv --- ncbi-tools6-6.1.20070822.orig/debian/libvibrant6-dev.install +++ ncbi-tools6-6.1.20070822/debian/libvibrant6-dev.install @@ -0,0 +1,85 @@ +usr/include/ncbi/aacomp.h +usr/include/ncbi/algorend.h +usr/include/ncbi/apparam.h +usr/include/ncbi/biosrc.h +usr/include/ncbi/bspview.h +usr/include/ncbi/cdrgn.h +usr/include/ncbi/cn3d*.h +usr/include/ncbi/ddvclick.h +usr/include/ncbi/ddvcreate.h +usr/include/ncbi/ddvgraph.h +usr/include/ncbi/ddvmain.h +usr/include/ncbi/ddvopen.h +usr/include/ncbi/ddvpanel.h +usr/include/ncbi/diagnost.h +usr/include/ncbi/dlogutil.h +usr/include/ncbi/document.h +usr/include/ncbi/dotmatrx.h +usr/include/ncbi/dotviewer.h +usr/include/ncbi/drawingp.h +usr/include/ncbi/drawseq.h +usr/include/ncbi/entrez*.h +usr/include/ncbi/fea2seg.h +usr/include/ncbi/fstyle*.h +usr/include/ncbi/glbpic.h +usr/include/ncbi/gphdraw.h +usr/include/ncbi/gtrdraw.h +usr/include/ncbi/gxydraw.h +usr/include/ncbi/image*.h +usr/include/ncbi/import.h +usr/include/ncbi/ingen*.h +usr/include/ncbi/layout.h +usr/include/ncbi/legend.h +usr/include/ncbi/mapgene.h +usr/include/ncbi/mappingp.h +usr/include/ncbi/medview.h +usr/include/ncbi/motif.h +usr/include/ncbi/ncbidraw.h +usr/include/ncbi/ncbigif.h +usr/include/ncbi/ncbiport.h +usr/include/ncbi/netscape.h +usr/include/ncbi/odlbox.h +usr/include/ncbi/panels.h +usr/include/ncbi/pictur*.h +usr/include/ncbi/ppict3d.h +usr/include/ncbi/prtgene.h +usr/include/ncbi/pubdesc.h +usr/include/ncbi/saldist.h +usr/include/ncbi/saled.h +usr/include/ncbi/saledit.h +usr/include/ncbi/salfiles.h +usr/include/ncbi/salogif.h +usr/include/ncbi/salpanel.h +usr/include/ncbi/salparam.h +usr/include/ncbi/sdisplay.h +usr/include/ncbi/seqanal.h +usr/include/ncbi/seqcons.h +usr/include/ncbi/seqfltr.h +usr/include/ncbi/seqgraph.h +usr/include/ncbi/seqgrphx.h +usr/include/ncbi/seqmtrx.h +usr/include/ncbi/seqpanel.h +usr/include/ncbi/seqpcc.h +usr/include/ncbi/seqscrl.h +usr/include/ncbi/seqsub.h +usr/include/ncbi/shim3d.h +usr/include/ncbi/treevi*.h +usr/include/ncbi/udvdef.h +usr/include/ncbi/udviewer.h +usr/include/ncbi/udvseq.h +usr/include/ncbi/urkgraph.h +usr/include/ncbi/vib*.h +usr/include/ncbi/viewer*.h +usr/include/ncbi/vsm*.h +usr/lib/libddvlib.a +usr/lib/libddvlib.so +usr/lib/libncbicn3d*.a +usr/lib/libncbicn3d*.so +usr/lib/libncbidesk.a +usr/lib/libncbidesk.so +usr/lib/libvibgif.a +usr/lib/libvibgif.so +usr/lib/libvibnet.a +usr/lib/libvibnet.so +usr/lib/libvibrant*.a +usr/lib/libvibrant*.so --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-bin.install +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-bin.install @@ -0,0 +1,30 @@ +usr/bin/asn2all +usr/bin/asn2asn +usr/bin/asn2fsa +usr/bin/asn2ff +usr/bin/asn2gb +usr/bin/asn2idx +usr/bin/asn2xml +usr/bin/asndhuff +usr/bin/asnval +usr/bin/checksub +usr/bin/cleanasn +usr/bin/debruijn +usr/bin/fa2htgs +usr/bin/findspl +usr/bin/gbseqget +usr/bin/gene2xml +usr/bin/getmesh +usr/bin/getpub +usr/bin/gil2bin +usr/bin/idfetch +usr/bin/indexpub +usr/bin/insdseqget +usr/bin/makeset +usr/bin/nps2gps +usr/bin/sortbyquote +usr/bin/spidey +usr/bin/tbl2asn +usr/bin/trna2sap +usr/bin/trna2tbl +usr/bin/vecscreen --- ncbi-tools6-6.1.20070822.orig/debian/compat +++ ncbi-tools6-6.1.20070822/debian/compat @@ -0,0 +1 @@ +5 --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6.examples +++ ncbi-tools6-6.1.20070822/debian/libncbi6.examples @@ -0,0 +1 @@ +doc/fwd_check.sh --- ncbi-tools6-6.1.20070822.orig/debian/blast2.docs +++ ncbi-tools6-6.1.20070822/debian/blast2.docs @@ -0,0 +1,2 @@ +doc/blast/*.html +doc/blast/*.pdf --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.docs +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.docs @@ -0,0 +1,3 @@ +doc/fire* +doc/images +doc/sequin.htm --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.mime +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.mime @@ -0,0 +1,2 @@ +chemical/ncbi-asn1-binary; viewer=/usr/bin/Cn3D-3.0 %s; test=test -n "$DISPLAY" +chemical/ncbi-asn1-text; viewer=/usr/bin/Cn3D-3.0 %s; test=test -n "$DISPLAY" --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.links +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.links @@ -0,0 +1,4 @@ +usr/bin/entrez2 usr/bin/entrez +usr/bin/Psequin usr/bin/sequin +usr/share/man/man1/entrez2.1 usr/share/man/man1/entrez.1 +usr/share/man/man1/Psequin.1 usr/share/man/man1/sequin.1 --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6.doc-base +++ ncbi-tools6-6.1.20070822/debian/libncbi6.doc-base @@ -0,0 +1,13 @@ +Document: ncbi-tools-dispatcher +Title: NCBI Dispatcher Parameters +Author: The National Center for Biotechnology Information +Abstract: Problems connecting to NCBI databases may be due to the + presence of a firewall at your site, especially if you receive error + messages about the inability to connect to a dispatcher. This + document details how to configure clients to use firewalls, and how + to configure firewalls to let clients through. +Section: net + +Format: HTML +Index: /usr/share/doc/libncbi6/dispatcher.html +Files: /usr/share/doc/libncbi6/dispatcher.html --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-x11.prerm +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-x11.prerm @@ -0,0 +1,5 @@ +#!/bin/sh -e + +/usr/sbin/update-alternatives --remove Cn3D /usr/bin/Cn3D-3.0 + +#DEBHELPER# --- ncbi-tools6-6.1.20070822.orig/debian/.nlmstmanrc +++ ncbi-tools6-6.1.20070822/debian/.nlmstmanrc @@ -0,0 +1,646 @@ +[style1] +PPPPAAAA=AACAAAAE +PPPPAAAC=AAGAAAADAAAAAAAB +AAACAAAB=AAACAAPPAAPP +AAACAAAC=AAABAB +AAACAAAD=AAACAAAAPPAA +AAACAAAE=AAICAAPPAAAAAAAC +AAACAAAG=AACAAAAE +AAADAAAG=AACAAAAF +AAAEAAAG=AACAAAAI +AAAHAAAG=AACAAAAJ +AAAIAAAG=AACAAAAK +AAAJAAAG=AACAAAAL +AAAKAAAG=AACAAAAM +AAAMAAAG=AACAAAAA +AAANAAAG=AACAAAAN +AAAOAAAG=AACAAAAO +AAAPAAAG=AACAAAAP +AABAAAAG=AACAAABA +AABBAAAG=AACAAABB +AABCAAAG=AACAAABC +AABDAAAG=AACAAABD +AABEAAAG=AACAAABE +AABFAAAG=AACAAABF +AABGAAAG=AACAAABG +AABHAAAG=AACAAAAG +AABKAAAG=AACAAAAH +AABLAAAG=AACAAAAC +AABMAAAG=AACAAABI +AABNAAAG=AACAAABJ +AABOAAAG=AACAAABK +AABPAAAG=AACAAABL +AACAAAAG=AACAAABM +AACBAAAG=AACAAABN +AACCAAAG=AACAAABO +AACDAAAG=AACAAABP +AACEAAAG=AACAAACA +AACFAAAG=AACAAACB +AACGAAAG=AACAAACC +AACHAAAG=AACAAACD +AACIAAAG=AACAAACE +AACJAAAG=AACAAACF +AACKAAAG=AACAAACG +AACLAAAG=AACAAACH +AACMAAAG=AACAAAAB +AADBAAAG=AACAAAAF +AADCAAAF=AACAAAAE +AADCAAAG=AACAAAAE +AADDAAAG=AACAAAAD +AADEAAAG=AACAAACM +AADFAAAG=AACAAACN +AADGAAAG=AACAAACO +AADHAAAG=AACAAAAC +AADIAAAG=AACAAAAA +AADJAAAG=AACAAACP +AADKAAAG=AACAAADA +AADLAAAG=AACAAADB +AADMAAAG=AACAAADC +AADNAAAG=AACAAADD +AADOAAAG=AACAAADE +AADPAAAG=AACAAADF +AAEAAAAG=AACAAADG +AAEBAAAG=AACAAADH +AAECAAAG=AACAAADI +AAEDAAAG=AACAAADJ +AAEEAAAG=AACAAADK +AAEFAAAG=AACAAADL +AAEGAAAG=AACAAADM +AAEHAAAG=AACAAADN +AAEIAAAG=AACAAAAB +AAEKAAAG=AACAAADO +AAELAAAG=AACAAADP +AAEMAAAG=AACAAAEA +AAENAAAG=AACAAAEB +AAEOAAAG=AACAAAEC +AAEPAAAG=AACAAAED +AAFAAAAG=AACAAAEE +AAFBAAAG=AACAAAEF +AAFCAAAG=AACAAAEG +AAFDAAAG=AACAAAEI +AAFEAAAG=AACAAAEH +PPPPAAAE=EACAAAACexon-intron +AAAEAAAB=ABACAAPPAAAAAAAAAAAE +AAAEAAAE=AAICAAPPAAAAAAAC +PPPNAAAB=AAACAAAAPPPP +AAADAAAE=AAICAAAAIAAAAAAL +AAAFAAAB=ABACAAAAIAIAAAAAAAAE +AAAFAAAE=AAICAAPPAAAAAAAN +AABIAAAF=AACAAAAE +AABIAAAG=AACAAAAB +AABJAAAG=AACAAABH +AABLAAAF=AACAAAAE +AADDAAAF=AACAAAAE +AAAFAAAD=AAACAAPPAAPP +AAALAAAG=AACAAAAD +AAABAAAB=ABACAAAAPPPPAAAAAAAE +AAAFAAAF=AACAAAAB +AAAGAAAG=AACAAAAE +AACMAAAB=ABACAAAAIAIAAAAAAAAE +AACMAAAF=AACAAAAB +AABAAAAB=AAECAAPPAAPPAAAAAABD +AACKAAAB=AAECAAAAAAPPAAAAAABE +AACLAAAB=AAECAAAAAAPPAAAAAABE +AACPAAAB=AAECAAAAIAIAAAAAAABC +AADBAAAB=AAECAAPPAAAAAAAAAABC +AAEIAAAB=AAEAAAAAAABC +AAEHAAAB=AAECAAPPAAPPAAAAAABE +AAEHAAAE=AAACAAAAAAPP +PPPMAAAC=AAABAB +PPPMAAAE=AAMAAAAAAAAEAABD +AAADAAAD=AAACAAAAIAAA +AACMAAAD=AAECAAPPAAAAAAAAAAAC +PPPOAAAB=AABAAC +AAAAAAAE=AAGAAABEAAAAAAAC +AAAGAAAE=AAIAAAAP +PPPMAAAB=ABAAAAAAAAAG +AAADAAAC=AAACAAAAAAPP +PPPLAAAE=AAICAAAAIAAAAAAC +AAABAAAE=AAIAAAAO +PPPJAAAB=AAACAAPPAAAA +PPPJAAAE=AAICAAPPAAAAAAAK +PPPKAAAB=AAACAAAAAAPP +PPPKAAAE=AAICAAAAIAAAAAAJ +AAAAAAAB=ABAAAAAAAAAD +AAADAAAB=ABAAAAAAAAAE +AAAGAAAB=ABAAAAAAAAAE +AAAHAAAB=ABAAAAAAAAAE +AAAIAAAB=ABAAAAAAAAAE +AAAJAAAB=ABAAAAAAAAAE +AAAKAAAB=ABAAAAAAAAAE +AAANAAAB=ABAAAAAAAAAE +AAAOAAAB=ABAAAAAAAAAE +AAAPAAAB=ABAAAAAAAAAE +AABBAAAB=ABAAAAAAAAAE +AABCAAAB=ABAAAAAAAAAE +AABDAAAB=ABAAAAAAAAAE +AABEAAAB=ABAAAAAAAAAE +AABFAAAB=ABAAAAAAAAAE +AABGAAAB=ABAAAAAAAAAE +AABHAAAB=ABAAAAAAAAAE +AABIAAAB=ABACAAPPAAPPAAAAAAAE +AABIAAAE=AAIAAABB +AABJAAAB=ABAAAAAAAAAE +AABKAAAB=ABAAAAAAAAAE +AABLAAAB=ABACAAAAPPPPAAAAAAAE +AABLAAAE=AAIAAABB +AABMAAAB=ABAAAAAAAAAE +AABNAAAB=ABAAAAAAAAAE +AABOAAAB=ABAAAAAAAAAE +AABPAAAB=ABAAAAAAAAAE +AACAAAAB=ABAAAAAAAAAE +AACBAAAB=ABAAAAAAAAAE +AACCAAAB=ABAAAAAAAAAE +AACDAAAB=ABAAAAAAAAAE +AACEAAAB=ABAAAAAAAAAE +AACFAAAB=ABAAAAAAAAAE +AACMAAAE=AAIAAAAM +AADCAAAB=ABAAAAAAAAAE +AADCAAAE=AAIAAABB +AADDAAAB=ABAAAAAAAAAE +AADDAAAE=AAIAAABB +PPPNAAAE=AAACAAPPPPAA +AAEKAAAB=ABAAAAAAAAAE +AAEKAAAE=AAIAAABB + +[SYSTEM] +STYLE1=style1 +styles=3 +fonts=24 +STYLE2=style2 + +[SYSTEMFONT:2] +name=Times Roman +size=12 +style=0 +charset=1 +pitch=2 +family=1 + +[SYSTEMFONT:1] +name=Helvetica +size=12 +style=0 +charset=1 +pitch=2 +family=2 + +[SYSTEMFONT:3] +name=Courier +size=12 +style=0 +charset=1 +pitch=1 +family=3 + +[SYSTEMFONT:4] +name=Courier +size=12 +style=0 +charset=1 +pitch=1 +family=3 + +[SYSTEMFONT:7] +name=helvetica +size=14 +style=3 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:6] +name=Helvetica +size=12 +style=0 +charset=1 +pitch=2 +family=2 + +[SYSTEMFONT:5] +name=Courier +size=12 +style=0 +charset=1 +pitch=1 +family=3 + +[SYSTEMFONT:8] +name=courier +size=12 +style=3 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:10] +name=Helvetica +size=14 +style=0 +charset=1 +pitch=2 +family=2 + +[SYSTEMFONT:9] +name=courier +size=14 +style=3 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:11] +name=times +size=10 +style=1 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:17] +name=Courier +size=12 +style=0 +charset=1 +pitch=1 +family=3 + +[SYSTEMFONT:16] +name=serif +size=11 +style=0 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:15] +name=helvetica +size=10 +style=3 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:14] +name=helvetica +size=10 +style=2 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:13] +name=courier +size=10 +style=1 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:12] +name=helvetica +size=10 +style=1 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:18] +name=lucida bright +size=6 +style=0 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:19] +name=times +size=10 +style=0 +charset=0 +pitch=0 +family=0 + +[style2] +PPPMAAAE=AAMAAAAAAAAEAABI +PPPPAAAA=AACAAAAF +PPPPAAAC=AACAAAAF +AAABAAAB=ABACAAIAIAIAAAAAAAAG +AAABAAAD=AAEAAAAAAAAC +AAABAAAE=AAIAAABG +AAABAAAG=AACAAAAB +AAACAAAE=AAIAAABG +AAADAAAD=AAECAAPPAAPPAAAAAAAC +AAADAAAE=AAIAAABG +AAADAAAG=AACAAAAH +AAAFAAAB=ABACAAAAPPAAAAAAAAAG +AAAFAAAD=AAECAAAAPPAAAAAAAAAC +AAAFAAAE=AAIAAABG +AAAFAAAF=AACAAAAB +AAAFAAAG=AACAAAAF +AAAGAAAD=AAECAAAAAAPPAAAAAAAC +AAAGAAAE=AAIAAABG +AAAGAAAG=AACAAAAG +AAAHAAAB=ABACAAPPAAAAAAAAAAAG +AAAHAAAD=AAECAAPPAAAAAAAAAAAC +AAAHAAAE=AAIAAABG +AAAHAAAF=AACAAAAD +AAAHAAAG=AACAAAAF +AAAIAAAB=ABACAAPPAAAAAAAAAAAG +AAAIAAAD=AAECAAPPAAAAAAAAAAAC +AAAIAAAE=AAIAAABG +AAAIAAAF=AACAAAAD +AAAJAAAB=ABACAAPPAAAAAAAAAAAG +AAAJAAAD=AAECAAPPAAAAAAAAAAAC +AAAJAAAE=AAIAAABG +AAAJAAAF=AACAAAAD +AAAJAAAG=AACAAAAD +AAAKAAAB=ABACAAPPAAAAAAAAAAAG +AAAKAAAD=AAECAAPPAAAAAAAAAAAC +AAAKAAAE=AAIAAABG +AAAKAAAF=AACAAAAD +AAAKAAAG=AACAAAAC +AAALAAAE=AAIAAABG +AAAMAAAE=AAIAAABG +AAAMAAAG=AACAAAAA +AAANAAAG=AACAAAAB +AAAOAAAG=AACAAAAC +AAAPAAAE=AAIAAABG +AAAPAAAG=AACAAAAD +AABAAAAE=AAIAAABG +AABAAAAG=AACAAAAE +AABBAAAE=AAIAAABG +AABBAAAG=AACAAAAF +AABCAAAG=AACAAAAG +AABDAAAE=AAIAAABG +AABDAAAG=AACAAAAH +AABEAAAB=AAEAAAAAAABE +AABEAAAG=AACAAAAI +AABFAAAE=AAIAAABG +AABFAAAG=AACAAAAJ +AABGAAAE=AAIAAABG +AABGAAAG=AACAAAAK +AABHAAAB=AAEAAAAAAABE +AABHAAAE=AAIAAABG +AABHAAAG=AACAAAAL +AABIAAAE=AAIAAABG +AABIAAAG=AACAAAAM +AABJAAAB=AAEAAAAAAABE +AABJAAAE=AAIAAABG +AABJAAAG=AACAAAAN +AABKAAAE=AAIAAABG +AABKAAAG=AACAAAAO +AABLAAAE=AAIAAABG +AABLAAAG=AACAAAAP +AABMAAAE=AAIAAABG +AABMAAAG=AACAAABA +AABNAAAE=AAIAAABG +AABNAAAG=AACAAABB +AABOAAAE=AAIAAABG +AABOAAAG=AACAAABC +AABPAAAE=AAIAAABG +AABPAAAG=AACAAABD +AACAAAAB=AAEAAAAAAABE +AACAAAAE=AAIAAABG +AACAAAAG=AACAAABE +AACBAAAE=AAIAAABG +AACBAAAG=AACAAABF +AACCAAAE=AAIAAABG +AACCAAAG=AACAAABG +AACDAAAB=ABACAAPPAAAAAAAAAAAG +AACDAAAD=AAECAAPPAAAAAAAAAAAC +AACDAAAE=AAIAAABG +AACDAAAF=AACAAAAD +AACDAAAG=AACAAAAB +AACEAAAB=AAEAAAAAAABE +AACEAAAE=AAIAAABG +AACEAAAG=AACAAABH +AACFAAAB=AAEAAAAAAABE +AACFAAAE=AAIAAABG +AACFAAAG=AACAAABI +AACGAAAB=AAEAAAAAAABE +AACGAAAE=AAIAAABG +AACGAAAG=AACAAABJ +AACHAAAB=AAEAAAAAAABE +AACHAAAE=AAIAAABG +AACHAAAG=AACAAABK +AACIAAAE=AAIAAABG +AACIAAAG=AACAAABL +AACJAAAE=AAIAAABG +AACJAAAG=AACAAABM +AACKAAAB=AAEAAAAAAABF +AACKAAAE=AAIAAABG +AACKAAAG=AACAAABN +AACLAAAB=AAEAAAAAAABE +AACLAAAE=AAIAAABG +AACLAAAG=AACAAABO +AACMAAAF=AACAAAAB +AACMAAAG=AACAAAAE +AACNAAAE=AAIAAABG +AACNAAAG=AACAAAAD +AACOAAAE=AAIAAABG +AACOAAAG=AACAAABP +AACPAAAB=AAEAAAAAAABC +AACPAAAE=AAIAAABG +AACPAAAG=AACAAACA +AADAAAAB=AAEAAAAAAABE +AADAAAAE=AAIAAABG +AADAAAAG=AACAAACB +AADBAAAB=AAEAAAAAAABD +AADBAAAE=AAIAAABG +AADBAAAG=AACAAACC +AADCAAAE=AAIAAABG +AADCAAAG=AACAAACD +AADDAAAE=AAIAAABG +AADDAAAG=AACAAACE +AADEAAAB=AAECAAPPAAAAAAAAAABE +AADEAAAE=AAIAAABG +AADEAAAG=AACAAACF +AADFAAAE=AAIAAABG +AADFAAAG=AACAAACG +AADGAAAE=AAIAAABG +AADGAAAG=AACAAACH +AADHAAAE=AAIAAABG +AADHAAAG=AACAAACI +AADIAAAE=AAIAAABG +AADIAAAG=AACAAAAA +AADJAAAE=AAIAAABG +AADJAAAG=AACAAACJ +AADKAAAB=ABACAAAAIAIAAAAAAAAG +AADKAAAD=AAACAAAAIAIA +AADKAAAE=AAIAAABG +AADKAAAG=AACAAACK +AADLAAAB=AAECAAAAAAPPAAAAAABF +AADLAAAE=AAIAAABG +AADLAAAG=AACAAACL +AADMAAAB=AAECAAAAAAPPAAAAAABE +AADMAAAE=AAIAAABG +AADMAAAG=AACAAACM +AADNAAAE=AAIAAABG +AADNAAAG=AACAAACN +AADOAAAE=AAIAAABG +AADOAAAG=AACAAACO +AADPAAAE=AAIAAABG +AADPAAAG=AACAAACP +AAEAAAAE=AAIAAABG +AAEAAAAG=AACAAADA +AAEBAAAB=ABEAAAAAAABDAAAAAAAG +AAEBAAAE=AAIAAABG +AAEBAAAG=AACAAADB +AAECAAAE=AAIAAABG +AAECAAAG=AACAAADC +AAEDAAAE=AAIAAABG +AAEDAAAG=AACAAADD +AAEEAAAE=AAIAAABG +AAEEAAAG=AACAAADE +AAEFAAAE=AAIAAABG +AAEFAAAG=AACAAADF +AAEGAAAE=AAIAAABG +AAEGAAAG=AACAAADG +AAEHAAAB=AAEAAAAAAABE +AAEHAAAE=AAIAAABG +AAEHAAAG=AACAAADH +AAEIAAAB=AAEAAAAAAABE +AAEIAAAE=AAIAAABG +AAEIAAAG=AACAAADI +AAEKAAAE=AAIAAABG +AAEKAAAG=AACAAAAB +AAELAAAE=AAIAAABG +AAELAAAG=AACAAADJ +AAEMAAAE=AAIAAABG +AAEMAAAG=AACAAAAD +AAENAAAE=AAIAAABG +AAENAAAG=AACAAAAE +AAEOAAAB=AAEAAAAAAABE +AAEOAAAE=AAIAAABG +AAEOAAAG=AACAAADK +AAEPAAAE=AAIAAABG +AAEPAAAG=AACAAADL +AAFAAAAB=AAEAAAAAAABE +AAFAAAAE=AAIAAABG +AAFAAAAG=AACAAADM +AAFBAAAE=AAIAAABG +AAFBAAAG=AACAAADN +AAFCAAAE=AAIAAABG +AAFCAAAG=AACAAAAC +AAFDAAAB=AAEAAAAAAABE +AAFDAAAE=AAIAAABG +AAFDAAAG=AACAAAAB +AAFEAAAE=AAIAAABG +AAFEAAAG=AACAAAAC +PPPPAAAD=EACAAAAERNAs +PPPMAAAB=ABAAAAAAAAAI +AAAAAAAB=ABAAAAAAAAAD +AAAAAAAE=AAGAAABOAAAAAAAC +AAACAAAB=ABAAAAAAAAAG +AAADAAAB=ABAAAAAAAAAG +AAAEAAAB=ABACAAAAIAAAAAAAAAAG +AAAGAAAB=ABAAAAAAAAAG +AAALAAAB=ABAAAAAAAAAG +AAAMAAAB=ABAAAAAAAAAG +AAAPAAAB=ABAAAAAAAAAG +AABAAAAB=AAEAAAAAAABE +AABBAAAB=ABAAAAAAAAAG +AABCAAAB=AAEAAAAAAABE +AABDAAAB=ABAAAAAAAAAG +AABFAAAB=ABAAAAAAAAAG +AABGAAAB=ABAAAAAAAAAG +AABIAAAB=ABACAAIAIAIAAAAAAAAG +AABKAAAB=ABAAAAAAAAAG +AABLAAAB=ABACAAMAMAMAAAAAAAAG +AABMAAAB=ABAAAAAAAAAG +AABNAAAB=ABACAAIAAAAAAAAAAAAG +AABNAAAD=AAACAAIAAAAA +AABOAAAB=ABAAAAAAAAAG +AABPAAAB=ABAAAAAAAAAG +AACBAAAB=ABACAAAAIAIAAAAAAAAG +AACBAAAD=AAACAAAAIAIA +AACCAAAB=ABAAAAAAAAAG +AACIAAAB=ABAAAAAAAAAG +AACJAAAB=ABAAAAAAAAAG +AACMAAAB=ABAAAAAAAAAG +AACNAAAB=ABAAAAAAAAAG +AACNAAAF=AACAAAAB +AACOAAAB=ABACAAAAIAIAAAAAAAAG +AACOAAAD=AAACAAAAIAIA +AADCAAAB=ABAAAAAAAAAG +AADDAAAB=ABAAAAAAAAAG +AADFAAAB=ABAAAAAAAAAG +AADGAAAB=ABAAAAAAAAAG +AADHAAAB=ABAAAAAAAAAG +AADIAAAB=ABAAAAAAAAAG +AADJAAAB=ABAAAAAAAAAG +AADNAAAB=ABAAAAAAAAAG +AADOAAAB=ABEAAAAAAABEAAAAAAAG +AADPAAAB=ABAAAAAAAAAG +AAEAAAAB=ABAAAAAAAAAG +AAECAAAB=ABAAAAAAAAAG +AAEDAAAB=ABAAAAAAAAAG +AAEEAAAB=ABAAAAAAAAAG +AAEFAAAB=ABAAAAAAAAAG +AAEGAAAB=ABAAAAAAAAAG +AAEKAAAB=ABACAAAAIAIAAAAAAAAG +AAELAAAB=ABAAAAAAAAAG +AAEMAAAB=ABECAAPPAAAAAAAAAAAAAAAAAAAE +AAEMAAAD=AAECAAPPAAAAAAAAAAAC +AAENAAAB=AAECAAAAAAPPAAAAAABE +AAEPAAAB=ABAAAAAAAAAG +AAFBAAAB=ABAAAAAAAAAG +AAFCAAAB=ABACAAIAAAAAAAAAAAAG +PPPJAAAE=AAIAAABH +PPPKAAAE=AAICAAAAAAPPAABH +PPPLAAAE=AAICAAPPAAAAAABH +AAAEAAAE=AAIAAABH +AAAEAAAF=AACAAAAB +AAAEAAAG=AACAAAAC +AAEKAAAF=AACAAAAE +AAEMAAAF=AACAAAAF +AAENAAAF=AACAAAAF +AAFCAAAF=AACAAAAE +AAFDAAAF=AACAAAAF +AAFEAAAB=AAECAAIAAAIAAAAAAABC +AAFEAAAF=AACAAAAF +PPPPAAAE=EACAAAADProts +PPPPAAAF=EACAAAACProt1 + +[SYSTEMFONT:22] +name=lucida bright +size=10 +style=0 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:21] +name=helvetica +size=10 +style=0 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:20] +name=helvetica +size=12 +style=1 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:23] +name=lucidabright +size=10 +style=0 +charset=0 +pitch=0 +family=0 + +[SYSTEMFONT:24] +name=helvetica +size=12 +style=1 +charset=0 +pitch=0 +family=0 + + --- ncbi-tools6-6.1.20070822.orig/debian/ncbi-tools-bin.override +++ ncbi-tools6-6.1.20070822/debian/ncbi-tools-bin.override @@ -0,0 +1 @@ +ncbi-tools-bin: menu-icon-missing /usr/share/pixmaps/ncbilogo.xpm --- ncbi-tools6-6.1.20070822.orig/debian/entrez2.desktop.in +++ ncbi-tools6-6.1.20070822/debian/entrez2.desktop.in @@ -0,0 +1,3 @@ +Name=Entrez NCBI Database Querying Tool +GenericName=Database Querying Tool +Comment=Query NCBI databases and retrieve documents --- ncbi-tools6-6.1.20070822.orig/debian/libvibrant6a.override +++ ncbi-tools6-6.1.20070822/debian/libvibrant6a.override @@ -0,0 +1 @@ +libvibrant6a: package-name-doesnt-match-sonames --- ncbi-tools6-6.1.20070822.orig/debian/vibrate +++ ncbi-tools6-6.1.20070822/debian/vibrate @@ -0,0 +1,20 @@ +#!/bin/sh +if [ $# = 0 -o "x$1" = "x--help" ]; then + cat <&1 >/dev/null \ + | sed -e "/usr/d; s@^ *@$f: @" | sort -u +done --- ncbi-tools6-6.1.20070822.orig/debian/copyright +++ ncbi-tools6-6.1.20070822/debian/copyright @@ -0,0 +1,37 @@ +This package was originally debianized by Stephane Bortzmeyer + on Tue, 22 Sep 1998 17:23:12 +0200. +Subsequent maintainers have been Dr. Guenter Bechly + and Aaron M. Ucko , who +conveniently happens to work at NCBI. ;-) + +It was downloaded from ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/ + +The reference Web server is http://www.ncbi.nlm.nih.gov/BLAST/ + +The upstream authors are several: see the README. The contact address +is toolbox@ncbi.nlm.nih.gov. + + +Copyright: + +The NCBI toolkit has been put into the public domain, completely unfettered: + + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information + +This software/database is a "United States Government Work" under the +terms of the United States Copyright Act. It was written as part of +the author's official duties as a United States Government employee and +thus cannot be copyrighted. This software/database is freely available +to the public for use. The National Library of Medicine and the U.S. +Government have not placed any restriction on its use or reproduction. + +Although all reasonable efforts have been taken to ensure the accuracy +and reliability of the software and data, the NLM and the U.S. +Government do not and cannot warrant the performance or results that +may be obtained by using this software or data. The NLM and the U.S. +Government disclaim all warranties, express or implied, including +warranties of performance, merchantability or fitness for any particular +purpose. + +Please cite the author in any work or product based on this material. --- ncbi-tools6-6.1.20070822.orig/debian/libncbi6.install +++ ncbi-tools6-6.1.20070822/debian/libncbi6.install @@ -0,0 +1,12 @@ +usr/lib/libblast*.so.* +usr/lib/libncbi.so.* +usr/lib/libncbi*acc.so.* +usr/lib/libncbicdr.so.* +usr/lib/libncbiid1.so.* +usr/lib/libncbimla.so.* +usr/lib/libncbimmdb.so.* +usr/lib/libncbiobj.so.* +usr/lib/libncbitool.so.* +usr/lib/libncbitxc2.so.* +usr/lib/libnet*.so.* +usr/lib/libvibgif.so.* --- ncbi-tools6-6.1.20070822.orig/debian/Psequin.desktop.in +++ ncbi-tools6-6.1.20070822/debian/Psequin.desktop.in @@ -0,0 +1,3 @@ +Name=Sequin DNA Sequence Submission Tool +GenericName=Sequence Submission Tool +Comment=Submit DNA sequences to the GenBank, EMBL, and DDBJ databases --- ncbi-tools6-6.1.20070822.orig/debian/blast2.override +++ ncbi-tools6-6.1.20070822/debian/blast2.override @@ -0,0 +1 @@ +blast2: menu-icon-missing /usr/share/pixmaps/ncbilogo.xpm --- ncbi-tools6-6.1.20070822.orig/debian/libvibrant6a.install +++ ncbi-tools6-6.1.20070822/debian/libvibrant6a.install @@ -0,0 +1,5 @@ +usr/lib/libddvlib.so.* +usr/lib/libncbicn3d*.so.* +usr/lib/libncbidesk.so.* +usr/lib/libvibnet.so.* +usr/lib/libvibrant*.so.* --- ncbi-tools6-6.1.20070822.orig/debian/blast2.install +++ ncbi-tools6-6.1.20070822/debian/blast2.install @@ -0,0 +1,16 @@ +usr/bin/bl2seq +usr/bin/blast2 +usr/bin/blastall +usr/bin/blastall_old +usr/bin/blastcl3 +usr/bin/blastclust +usr/bin/blastpgp +usr/bin/copymat +usr/bin/fastacmd +usr/bin/formatdb +usr/bin/formatrpsdb +usr/bin/impala +usr/bin/makemat +usr/bin/megablast +usr/bin/rpsblast +usr/bin/seedtop --- ncbi-tools6-6.1.20070822.orig/debian/help2man +++ ncbi-tools6-6.1.20070822/debian/help2man @@ -0,0 +1,127 @@ +#!/usr/bin/perl -w +use strict; + +use POSIX qw(strftime); + +my $AUTHOR = 'Aaron M. Ucko '; + +# Generates initial Debian manpages based on help output ("-" flag). +# bod's help2man won't work here, since it assumes GNU conventions. + +# Sigh...vibrant and non-vibrant versions only agree on T/F, Integer, +# and String. +my %type_map = ( 'Data In' => 'filename', + 'Data Out' => 'filename', + 'File In' => 'filename', + 'File Out' => 'filename', + 'Float' => 'X', + 'Input-Data' => 'filename', + 'Input-File' => 'filename', + 'Integer' => 'N', + 'Output-Data' => 'filename', + 'Output-File' => 'filename', + 'Real' => 'X', + 'String' => 'str', + 'T/F' => undef ); + +foreach my $prog (@ARGV) { + my $base = $prog; + $base =~ s@.*/@@; + open(MAN, ">doc/man/$base.1") or die; + print MAN '.TH ', uc($base), ' 1 ', strftime('%Y-%m-%d', localtime), + " NCBI \"NCBI Tools User's Manual\"\n"; + print MAN ".SH NAME\n$base \\- ...\n"; + + my %options = parse_options($prog); + my $key; + + print MAN ".SH SYNOPSIS\n.B $base\n", synopsis(\%options); + print MAN <) { + if (/^ (-\S+)\s*(.*)/) { + $options{$last_option} = $last_description if defined $last_option; + $last_option = $1; + $last_description = "$2\n"; + } elsif (defined $last_option) { + $last_description .= $_; + } + } + + if (defined $last_option) { + $options{$last_option} = $last_description; + $options{'-'} = "Print usage message\n"; + } + + close(HELP); + + foreach my $key (keys %options) { + if ($options{$key} =~ s@(\[T/F\](\s+Optional)?)\s+default = T@$1@) { + $options{"$key\\ F"} = "NOT $options{$key}"; + delete $options{$key}; + } else { + $options{$key} =~ s@(\[T/F\](\s+Optional)?)(\s+default = F)?@$1@; + } + } + + return %options; +} + +sub synopsis +{ + my %options = %{$_[0]}; + my $result = ''; + + foreach my $key (sort keys %options) { + my $desc = $options{$key}; + my $optional = ($desc =~ /Optional/ || $desc =~ /default = / + || $key eq '-' || $desc =~ /\[T\/F\]/); + $result .= '[\|' if $optional; + $result .= format_arg($key, $desc); + $result .= '\|]' if $optional; + $result .= "\n"; + } + + return $result; +} + +sub format_arg +{ + my ($arg, $desc) = @_; + my $result = "\\fB\\$arg\\fP"; + if ($desc =~ /\[(.*?)\]/) { + my $contents = $type_map{$1}; + $result .= '\ \fI' . $contents . '\fP' if defined $contents; + } + return $result; +} --- ncbi-tools6-6.1.20070822.orig/network/id1arch/idfetch.c +++ ncbi-tools6-6.1.20070822/network/id1arch/idfetch.c @@ -204,6 +204,7 @@ static Boolean ProcessOneDocSum (Int4 num, Int4Ptr uids); static void EntrezQuery(char *query); +static int TryGetGi(int choice, char *accession, char *name, int version); static Int4 BEGetUidsFromQuery(CharPtr query, Uint4Ptr PNTR uids, Boolean is_na, Boolean count_only); --- ncbi-tools6-6.1.20070822.orig/vibrant/shim3d.c +++ ncbi-tools6-6.1.20070822/vibrant/shim3d.c @@ -327,7 +327,8 @@ #include #if defined(_OPENGL) && defined(_PNG) -TOGL_Data *Cn3D_GetCurrentOGLData(void); /* in cn3dxprt.c */ +/* In cn3dxprt.c; declared weak here to avoid dependency loops. */ +extern TOGL_Data *Cn3D_GetCurrentOGLData(void) __attribute__((weak)); #endif @@ -2711,6 +2712,9 @@ if (OGL_Data == NULL) return; + if (!OGL_Data->BoundBox.set) + OGL_ClearBoundBox(&(OGL_Data->BoundBox)); + OGL_Data->MaxSize = (Nlm_FloatLo) fabs(OGL_Data->BoundBox.x[0] - OGL_Data->BoundBox.x[1]); diff = fabs(OGL_Data->BoundBox.y[0] - OGL_Data->BoundBox.y[1]); @@ -2924,7 +2928,15 @@ png_structp png_ptr = NULL; png_infop info_ptr = NULL; Nlm_Boolean doInterlacing = TRUE; - TOGL_Data *OGL_Data = (TOGL_Data *)(Cn3D_GetCurrentOGLData()); + TOGL_Data *OGL_Data; + + if (!Cn3D_GetCurrentOGLData) { + Message(MSG_ERROR, "PNG output unavailable; " + "please relink application with -lncbicn3d."); + return; + } + + OGL_Data = (TOGL_Data *)(Cn3D_GetCurrentOGLData()); #if defined(WIN_MOTIF) GLint glSize; @@ -3705,4 +3717,3 @@ if (fblock) MemFree(fblock); } - --- ncbi-tools6-6.1.20070822.orig/vibrant/vibwndws.c +++ ncbi-tools6-6.1.20070822/vibrant/vibwndws.c @@ -7109,7 +7109,7 @@ Nlm_InitPrompt (); Nlm_InitSlate (); Nlm_InitTexts (); - if (! Nlm_SetupWindows ()) return; + if (! Nlm_SetupWindows ()) exit(1); Nlm_RegisterWindows (); Nlm_RegisterTexts (); Nlm_RegisterSlates (); --- ncbi-tools6-6.1.20070822.orig/vibrant/vibmain.c +++ ncbi-tools6-6.1.20070822/vibrant/vibmain.c @@ -44,6 +44,21 @@ +extern Nlm_Int2 Nlm_Main(void) __attribute__((weak)); + +static Nlm_Int2 s_CallNlmMain(void) +{ + if (Nlm_Main) { + return Nlm_Main(); + } else { + ErrPost(0, 0, "Neither main nor Nlm_Main defined by program."); + return -1; + } +} + +#define Nlm_Main s_CallNlmMain + + #ifdef WIN_MAC #ifdef OS_UNIX_DARWIN int main (int argc, char *argv[]) --- ncbi-tools6-6.1.20070822.orig/vibrant/netscape.c +++ ncbi-tools6-6.1.20070822/vibrant/netscape.c @@ -548,9 +548,8 @@ } /* ---------- child process ------------ */ - if (execlp("netscape", "netscape", url, NULL) < 0 && - execl(NETSCAPE_PATH, NETSCAPE_PATH, url, NULL) < 0) { - Message(MSG_ERROR, "Failure to open URL in netscape window"); + if (execlp("sensible-browser", "sensible-browser", url, NULL) < 0) { + Message(MSG_ERROR, "Failure to open URL in browser window"); exit(1); }