To see what ports are currently on, and their status, as reported within -NCBI, please refer to the following Firewall Daemon Presence +NCBI, please refer to the following Firewall Daemon Presence Check page. Ports marked INTERNAL are solely for NCBI own use, and may be inaccessible from your site. That, however, does not affect availability of any services that NCBI provides through other (open) firewall ports. @@ -143,7 +143,7 @@ your host just by running simple telnet command (available on most current systems). To know which ports, at the moment, you should be trying from the list above (see the "Ports to open"), first check their status by visiting -Firewall Daemon Presence Check link, then select any +Firewall Daemon Presence Check link, then select any up-and-running port and do the following (the example assumes port 5861 has been shown in operational state):
@@ -175,7 +175,7 @@There is also an auxiliary automated UNIX shell script -fwd_check.sh to check all of +fwd_check.sh to check all of the preset ports, and it is kept in-sync with currently configured open ports (so remember to refresh your download prior to actual use). --- ncbi-tools6-6.1.20120620.orig/doc/fwd_check.sh +++ ncbi-tools6-6.1.20120620/doc/fwd_check.sh @@ -8,7 +8,7 @@ delay_sec="$1" delay_sec=${delay_sec:="10"} netcat="`which netcat 2>/dev/null`" -temp="/tmp/`basename $0`.$$.tmp" +temp=`mktemp` helper="./fwd_failure_helper.exe" test -z "$netcat" && netcat="`whereis netcat | sed 's/^[^:]*://;s/ //g'`" --- ncbi-tools6-6.1.20120620.orig/doc/man/Psequin.1 +++ ncbi-tools6-6.1.20120620/doc/man/Psequin.1 @@ -1,4 +1,4 @@ -.TH PSEQUIN 1 2005-11-04 NCBI "NCBI Tools User's Manual" +.TH PSEQUIN 1 2011-09-02 NCBI "NCBI Tools User's Manual" .SH NAME Psequin \- submit sequences to Genbank, EMBL, and DDBJ .SH SYNOPSIS @@ -91,6 +91,7 @@ The National Center for Biotechnology Information. .SH SEE ALSO .ad l +.BR asnmacro (1), .BR sbtedit (1), .BR tbl2asn (1), sequin.htm, --- ncbi-tools6-6.1.20120620.orig/doc/man/asn2all.1 +++ ncbi-tools6-6.1.20120620/doc/man/asn2all.1 @@ -1,10 +1,15 @@ -.TH ASN2ALL 1 2009-07-31 NCBI "NCBI Tools User's Manual" +.TH ASN2ALL 1 2012-06-24 NCBI "NCBI Tools User's Manual" .SH NAME asn2all \- generate reports from ASN.1 biological data .SH SYNOPSIS .B asn2all [\|\fB\-\fP\|] [\|\fB\-A\fP\ \fIacc\fP\|] +[\|\fB\-F\fP\ \fIfilename\fP\|] +[\|\fB\-G\fP\|] +[\|\fB\-J\fP\ \fIn\fP\|] +[\|\fB\-K\fP\ \fIn\fP\|] +[\|\fB\-M\fP\|] [\|\fB\-T\fP\|] [\|\fB\-X\fP\|] [\|\fB\-a\fP\ \fItype\fP\|] @@ -65,8 +70,26 @@ \fB\-\fP Print usage message .TP -\fB\-A\fP\ \fIacc\fP -Accession to fetch +\fB\-A\fP\ \fIaccession\fP +Accession to fetch; may take the form +.IB accession , complexity , flags +where \fIcomplexity\fP should normally be \fB0\fP and a \fIflags\fP +value of \fB-1\fP enables fetching of external features +.TP +\fB\-F\fP\ \fIfilename\fP +Accession Filter file +.TP +\fB\-G\fP +Relaxed Genome Mapping +.TP +\fB\-J\fP\ \fIn\fP +Seq-loc from +.TP +\fB\-K\fP\ \fIn\fP +Seq-loc to +.TP +\fB\-M\fP +Seq-loc Minus strand .TP \fB\-T\fP Use Threads @@ -80,6 +103,8 @@ .PD 0 .IP a Automatic (default) +.IP c +Catenated .IP z Any .IP e @@ -110,10 +135,14 @@ .PD 0 .IP g GenBank/GenPept (default) +.IP m +GenBank Master Style .IP f FASTA .IP d CDS FASTA +.IP e +Gene FASTA .IP t Sequin-style 5-column feature table .IP y --- ncbi-tools6-6.1.20120620.orig/doc/man/asn2fsa.1 +++ ncbi-tools6-6.1.20120620/doc/man/asn2fsa.1 @@ -1,4 +1,4 @@ -.TH ASN2FSA 1 2009-07-31 NCBI "NCBI Tools User's Manual" +.TH ASN2FSA 1 2011-09-02 NCBI "NCBI Tools User's Manual" .SH NAME asn2fsa \- convert biological sequence data from ASN.1 to FASTA .SH SYNOPSIS @@ -6,6 +6,8 @@ [\|\fB\-\fP\|] [\|\fB\-A\fP\ \fIacc\fP\|] [\|\fB\-D\fP\|] +[\|\fB\-E\fP\|] +[\|\fB\-H\fP\|] [\|\fB\-L\fP\ \fIfilename\fP\|] [\|\fB\-T\fP\|] [\|\fB\-a\fP\ \fItype\fP\|] @@ -43,6 +45,12 @@ \fB\-D\fP Use Dash for Gap .TP +\fB\-E\fP +Extended Seq-ids +.TP +\fB\-H\fP +HTML spans +.TP \fB\-L\fP\ \fIfilename\fP Log file .TP --- ncbi-tools6-6.1.20120620.orig/doc/man/asn2gb.1 +++ ncbi-tools6-6.1.20120620/doc/man/asn2gb.1 @@ -1,4 +1,4 @@ -.TH ASN2GB 1 2009-07-31 NCBI "NCBI Tools User's Manual" +.TH ASN2GB 1 2011-09-02 NCBI "NCBI Tools User's Manual" .SH NAME asn2gb \- convert ASN.1 biological data to a GenBank-style flat format .SH SYNOPSIS @@ -39,10 +39,15 @@ Print usage message .TP \fB\-A\fP\ \fIaccession\fP -Accession to fetch +Accession to fetch; may take the form +.IB accession , complexity , flags +where \fIcomplexity\fP should normally be \fB0\fP and a \fIflags\fP +value of \fB-1\fP enables fetching of external features (as with the +legacy \fB-F\fP option) .TP \fB\-F\fP -Fetch remote annotations +Fetch remote annotations (equivalent to specifying +\fB-A\fP\ \fIaccession\fP\fB,0,-1\fP) .TP \fB\-a\fP\ \fIasn-type\fP ASN.1 Type: --- ncbi-tools6-6.1.20120620.orig/doc/man/asndisc.1 +++ ncbi-tools6-6.1.20120620/doc/man/asndisc.1 @@ -0,0 +1,244 @@ +.TH ASNDISC 1 2012-06-24 NCBI "NCBI Tools User's Manual" +.SH NAME +asndisc \- check ASN.1 biological sequence records for discrepancies +.SH SYNOPSIS +.B asndisc +[\|\fB\-\fP\|] +[\|\fB\-B\fP\|] +[\|\fB\-C\fP\ \fIN\fP\|] +[\|\fB\-F\fP\|] +[\|\fB\-I\fP\ \fIpath\fP\|] +[\|\fB\-L\fP\ \fIstr\fP\|] +[\|\fB\-N\fP\ \fIfilename\fP\|] +[\|\fB\-P\fP\ \fIstr\fP\|] +[\|\fB\-R\fP\|] +[\|\fB\-S\fP\|] +[\|\fB\-T\fP\|] +[\|\fB\-X\fP\ \fItests\fP\|] +[\|\fB\-Z\fP\|] +[\|\fB\-a\fP\ \fIstr\fP\|] +[\|\fB\-b\fP\|] +[\|\fB\-c\fP\|] +[\|\fB\-d\fP\ \fItests\fP\|] +[\|\fB\-e\fP\ \fItests\fP\|] +[\|\fB\-f\fP\|] +[\|\fB\-i\fP\ \fIfilename\fP\|] +[\|\fB\-k\fP\|] +[\|\fB\-l\fP\|] +[\|\fB\-o\fP\ \fIfilename\fP\|] +[\|\fB\-p\fP\ \fIpath\fP\|] +[\|\fB\-r\fP\ \fIdir\fP\|] +[\|\fB\-s\fP\ \fIext\fP\|] +[\|\fB\-t\fP\|] +[\|\fB\-u\fP\|] +[\|\fB\-w\fP\ \fIfilename\fP\|] +[\|\fB\-x\fP\ \fIstr\fP\|] +.SH DESCRIPTION +\fBasndisc\fP is a command-line tool to check ASN.1-format biological +sequence records for discrepancies. +.SH OPTIONS +A summary of options is included below. +.TP +\fB\-\fP +Print usage message +.TP +\fB\-B\fP +Big sequence report +.TP +\fB\-C\fP\ \fIN\fP +Max count +.TP +\fB\-F\fP +Fix product name list +.TP +\fB\-I\fP\ \fIpath\fP +Path to Indexed binary ASN.1 data +.TP +\fB\-L\fP\ \fIstr\fP +Lineage to use +.TP +\fB\-N\fP\ \fIfilename\fP +File with list of product names to check +.TP +\fB\-P\fP\ \fIstr\fP +RePort type +.RS +.PD 0 +.IP g +Genome +.IP b +Big sequence +.IP m +MegaReport +.IP t +Include Tag +.IP s +Tag for Superuser +.PD +.RE +.TP +\fB\-R\fP +Remote fetching from ID +.TP +\fB\-S\fP +Summary report +.TP +\fB\-T\fP +Use threads +.TP +\fB\-X\fP\ \fItests\fP +EXpand report categories (comma-delimited list of test names as listed +below or ALL). +.TP +\fB\-Z\fP +Remote CDS Product Fetch +.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 bioseq-set +.IP u +batch seq-sUbmit +.PD +.RE +.TP +\fB\-b\fP +Batch file is Binary +.TP +\fB\-c\fP +Batch file is Compressed +.TP +\fB\-d\fP\ \fIstr\fP +Disable tests (comma-delimited list of test names as listed below). +.TP +\fB\-e\fP\ \fIstr\fP +Enable tests (comma-delimited list of test names as listed below). +.TP +\fB\-f\fP +Use Feature table output format +.TP +\fB\-i\fP\ \fIfilename\fP +Single input file (standard input by default) +.TP +\fB\-k\fP +Local fetching +.TP +\fB\-l\fP +Load components in advance +.TP +\fB\-o\fP\ \fIfilename\fP +Single output file +.TP +\fB\-p\fP\ \fIpath\fP +Path to ASN.1 files +.TP +\fB\-r\fP\ \fIdir\fP +Output directory +.TP +\fB\-s\fP\ \fIext\fP +Output file Suffix (\fB.dr\fP by default) +.TP +\fB\-t\fP +Big Test Set +.TP +\fB\-u\fP +Recurse +.TP +\fB\-w\fP\ \fIfilename\fP +Suspect product rule filename +.TP +\fB\-x\fP\ \fIstr\fP +File selection substring (\fB.sqn\fP by default) +.SS AVAILABLE TESTS +.P +.ad l +.nh +MISSING_GENES, EXTRA_GENES, MISSING_LOCUS_TAGS, DUPLICATE_LOCUS_TAGS, +BAD_LOCUS_TAG_FORMAT, INCONSISTENT_LOCUS_TAG_PREFIX, NON_GENE_LOCUS_TAG, +DISC_COUNT_NUCLEOTIDES, MISSING_PROTEIN_ID, INCONSISTENT_PROTEIN_ID, +FEATURE_LOCATION_CONFLICT, GENE_PRODUCT_CONFLICT, DUPLICATE_GENE_LOCUS, +EC_NUMBER_NOTE, PSEUDO_MISMATCH, JOINED_FEATURES, OVERLAPPING_GENES, +OVERLAPPING_CDS, CONTAINED_CDS, RNA_CDS_OVERLAP, SHORT_CONTIG, +INCONSISTENT_BIOSOURCE, SUSPECT_PRODUCT_NAMES, DISC_PRODUCT_NAME_TYPO, +DISC_PRODUCT_NAME_QUICKFIX, INCONSISTENT_SOURCE_DEFLINE, +PARTIAL_CDS_COMPLETE_SEQUENCE, EC_NUMBER_ON_UNKNOWN_PROTEIN, +TAX_LOOKUP_MISSING, TAX_LOOKUP_MISMATCH, SHORT_SEQUENCES, SUSPECT_PHRASES, +DISC_SUSPICIOUS_NOTE_TEXT, COUNT_TRNAS, FIND_DUP_TRNAS, FIND_BADLEN_TRNAS, +FIND_STRAND_TRNAS, COUNT_RRNAS, FIND_DUP_RRNAS, RNA_NO_PRODUCT, +TRANSL_NO_NOTE, NOTE_NO_TRANSL, TRANSL_TOO_LONG, CDS_TRNA_OVERLAP, +COUNT_PROTEINS, DISC_FEAT_OVERLAP_SRCFEAT, MISSING_GENPRODSET_PROTEIN, +DUP_GENPRODSET_PROTEIN, MISSING_GENPRODSET_TRANSCRIPT_ID, +DISC_DUP_GENPRODSET_TRANSCRIPT_ID, DISC_PERCENT_N, N_RUNS, ZERO_BASECOUNT, +ADJACENT_PSEUDOGENES, NO_ANNOTATION, DISC_INFLUENZA_DATE_MISMATCH, +DISC_SHORT_INTRON, DISC_MISSING_VIRAL_QUALS, DISC_SRC_QUAL_PROBLEM, +DISC_MISSING_SRC_QUAL, DISC_DUP_SRC_QUAL, DISC_DUP_SRC_QUAL_DATA, +DISC_HAPLOTYPE_MISMATCH, DISC_FEATURE_MOLTYPE_MISMATCH, +DISC_CDS_WITHOUT_MRNA, DISC_EXON_INTRON_CONFLICT, DISC_FEATURE_COUNT, +DISC_SPECVOUCHER_TAXNAME_MISMATCH, DISC_GENE_PARTIAL_CONFLICT, +DISC_FLATFILE_FIND_ONCALLER, DISC_CDS_PRODUCT_FIND, DISC_DUP_DEFLINE, +DUP_DISC_ATCC_CULTURE_CONFLICT, DISC_USA_STATE, DISC_INCONSISTENT_MOLTYPES, +DISC_SUBMITBLOCK_CONFLICT, DISC_POSSIBLE_LINKER, +DISC_TITLE_AUTHOR_CONFLICT, DISC_BAD_GENE_STRAND, +DISC_MAP_CHROMOSOME_CONFLICT, DISC_RBS_WITHOUT_GENE, +DISC_CITSUBAFFIL_CONFLICT, DISC_REQUIRED_CLONE, DISC_SOURCE_QUALS_ASNDISC, +DISC_mRNA_ON_WRONG_SEQUENCE_TYPE, DISC_RETROVIRIDAE_DNA, +DISC_CHECK_AUTH_CAPS, DISC_CHECK_RNA_PRODUCTS_AND_COMMENTS, +DISC_MICROSATELLITE_REPEAT_TYPE, DISC_MITOCHONDRION_REQUIRED, +DISC_UNPUB_PUB_WITHOUT_TITLE, DISC_QUALITY_SCORES, +DISC_INTERNAL_TRANSCRIBED_SPACER_RRNA, DISC_PARTIAL_PROBLEMS, +DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS, +DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION, DISC_SUSPECT_RRNA_PRODUCTS, +DISC_SUSPECT_MISC_FEATURES, DISC_BACTERIA_MISSING_STRAIN, +DISC_MISSING_DEFLINES, DISC_MISSING_AFFIL, +DISC_BACTERIA_SHOULD_NOT_HAVE_ISOLATE, DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA, +DISC_CDS_HAS_NEW_EXCEPTION, DISC_TRINOMIAL_SHOULD_HAVE_QUALIFIER, +DISC_METAGENOMIC, DISC_METAGENOME_SOURCE, ONCALLER_GENE_MISSING, +ONCALLER_SUPERFLUOUS_GENE, DISC_SHORT_RRNA, ONCALLER_CHECK_AUTHORITY, +ONCALLER_CONSORTIUM, ONCALLER_STRAIN_CULTURE_COLLECTION_MISMATCH, +ONCALLER_MULTISRC, ONCALLER_MULTIPLE_CULTURE_COLLECTION, +DISC_SEGSETS_PRESENT, DISC_NONWGS_SETS_PRESENT, DISC_FEATURE_LIST, +DISC_CATEGORY_HEADER, DISC_MISMATCHED_COMMENTS, +DISC_STRAIN_TAXNAME_MISMATCH, DISC_HUMAN_HOST, +DISC_BAD_BACTERIAL_GENE_NAME, TEST_BAD_GENE_NAME, ONCALLER_ORDERED_LOCATION, +ONCALLER_COMMENT_PRESENT, ONCALLER_DEFLINE_ON_SET, +ONCALLER_HIV_RNA_INCONSISTENT, SHORT_PROT_SEQUENCES, TEST_EXON_ON_MRNA, +TEST_HAS_PROJECT_ID, ONCALLER_HAS_STANDARD_NAME, +ONCALLER_MISSING_STRUCTURED_COMMENTS, DISC_REQUIRED_STRAIN, +MISSING_GENOMEASSEMBLY_COMMENTS, DISC_BACTERIAL_TAX_STRAIN_MISMATCH, +TEST_CDS_HAS_CDD_XREF, TEST_UNUSUAL_NT, TEST_LOW_QUALITY_REGION, +TEST_ORGANELLE_NOT_GENOMIC, TEST_UNWANTED_SPACER, TEST_ORGANELLE_PRODUCTS, +TEST_SP_NOT_UNCULTURED, TEST_BAD_MRNA_QUAL, TEST_UNNECESSARY_ENVIRONMENTAL, +TEST_UNNECESSARY_VIRUS_GENE, TEST_UNWANTED_SET_WRAPPER, TEST_MISSING_PRIMER, +TEST_UNUSUAL_MISC_RNA, TEST_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE, +TEST_DUP_GENES_OPPOSITE_STRANDS, TEST_SMALL_GENOME_SET_PROBLEM, +TEST_OVERLAPPING_RRNAS, TEST_MRNA_SEQUENCE_MINUS_STRAND_FEATURES, +TEST_TAXNAME_NOT_IN_DEFLINE, TEST_COUNT_UNVERIFIED, SHOW_TRANSL_EXCEPT, +SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME, TEST_DEFLINE_PRESENT, +TEST_MRNA_OVERLAPPING_PSEUDO_GENE, FIND_OVERLAPPED_GENES, +DISC_BIOMATERIAL_TAXNAME_MISMATCH, DISC_CULTURE_TAXNAME_MISMATCH, +DISC_CHECK_AUTH_NAME, NON_RETROVIRIDAE_PROVIRAL, RNA_PROVIRAL, +SHORT_SEQUENCES_200, DISC_10_PERCENTN, N_RUNS_14, MOLTYPE_NOT_MRNA, +TECHNIQUE_NOT_TSA, MISSING_STRUCTURED_COMMENT, MISSING_PROJECT, +MULTIPLE_CDS_ON_MRNA, DUP_DISC_CBS_CULTURE_CONFLICT, +DIVISION_CODE_CONFLICTS, RRNA_NAME_CONFLICTS, EUKARYOTE_SHOULD_HAVE_MRNA, +MRNA_SHOULD_HAVE_PROTEIN_TRANSCRIPT_IDS, ONCALLER_COUNTRY_COLON, +ONCALLER_BIOPROJECT_ID, ONCALLER_STRAIN_TAXNAME_CONFLICT +.hy +.ad b +.SH AUTHOR +The National Center for Biotechnology Information. +.SH SEE ALSO +.BR asnval (1), +.BR cleanasn (1). --- ncbi-tools6-6.1.20120620.orig/doc/man/asnmacro.1 +++ ncbi-tools6-6.1.20120620/doc/man/asnmacro.1 @@ -0,0 +1,60 @@ +.TH ASNMACRO 1 2011-09-02 NCBI "NCBI Tools User's Manual" +.SH NAME +asnmacro \- process ASN.1 biological data per Sequin macros +.SH SYNOPSIS +.B asnmacro +[\|\fB\-\fP\|] +[\|\fB\-b\fP\|] +[\|\fB\-d\fP\|] +[\|\fB\-e\fP\|] +[\|\fB\-i\fP\ \fIfilename\fP\|] +\|\fB\-m\fP\ \fIfilename\fP +[\|\fB\-o\fP\ \fIfilename\fP\|] +[\|\fB\-p\fP\ \fIpath\fP\|] +[\|\fB\-r\fP\ \fIpath\fP\|] +[\|\fB\-s\fP\ \fIstr\fP\|] +[\|\fB\-x\fP\ \fIstr\fP\|] +.SH DESCRIPTION +\fBasnmacro\fP is a command-line tool to run Sequin macros on +annotated biological sequence data represented according to NCBI's +ASN.1 specifications. +.SH OPTIONS +A summary of options is included below. +.TP +\fB\-\fP +Print usage message +.TP +\fB\-b\fP +Input is Binary +.TP +\fB\-d\fP +Output is binary +.TP +\fB\-e\fP +Input is a Seq-Entry +.TP +\fB\-i\fP\ \fIfilename\fP +Single input file +.TP +\fB\-m\fP\ \fIfilename\fP +Macro file +.TP +\fB\-o\fP\ \fIfilename\fP +Single Output file +.TP +\fB\-p\fP\ \fIpath\fP +Path to multiple input files +.TP +\fB\-r\fP\ \fIpath\fP +Path for Results when processing multiple files +.TP +\fB\-s\fP\ \fIstr\fP +Suffix for stripped (output) files +.TP +\fB\-x\fP\ \fIstr\fP +Suffix for input files with \fB-p\fP (\fB.sqn\fP by default) +.SH AUTHOR +The National Center for Biotechnology Information. +.SH SEE ALSO +.ad l +.BR Psequin (1). --- ncbi-tools6-6.1.20120620.orig/doc/man/asntool.1 +++ ncbi-tools6-6.1.20120620/doc/man/asntool.1 @@ -1,4 +1,4 @@ -.TH ASNTOOL 1 2005-05-16 NCBI "NCBI Tools User's Manual" +.TH ASNTOOL 1 2010-09-01 NCBI "NCBI Tools User's Manual" .SH NAME asntool \- process ASN.1 module specifications .SH SYNOPSIS @@ -13,6 +13,7 @@ [\|\fB\-L\fP\ \fIstr\fP\|] [\|\fB\-M\fP\ \fIfilename,...\fP\|] [\|\fB\-P\fP\ \fIstr\fP\|] +[\|\fB\-Q\fP\|] [\|\fB\-S\fP\ \fIfilename\fP\|] [\|\fB\-T\fP\ \fIfilename\fP\|] [\|\fB\-V\fP\|] @@ -77,6 +78,9 @@ \fB\-P\fP\ \fIstr\fP XML module prefix for \fBDOCTYPE\fP .TP +\fB\-Q\fP +Use quoted syntax form for generated include files +.TP \fB\-S\fP\ \fIfilename\fP Send debugging output to \fIfilename\fP rather than stderr .TP --- ncbi-tools6-6.1.20120620.orig/doc/man/asnval.1 +++ ncbi-tools6-6.1.20120620/doc/man/asnval.1 @@ -1,4 +1,4 @@ -.TH ASNVAL 1 2009-07-31 NCBI "NCBI Tools User's Manual" +.TH ASNVAL 1 2012-06-24 NCBI "NCBI Tools User's Manual" .SH NAME asnval \- validate ASN.1 biological sequence records .SH SYNOPSIS @@ -7,7 +7,9 @@ [\|\fB\-A\fP\|] [\|\fB\-B\fP\|] [\|\fB\-C\fP\ \fIN\fP\|] +[\|\fB\-D\fP\|] [\|\fB\-E\fP\ \fIstr\fP\|] +[\|\fB\-F\fP\|] [\|\fB\-G\fP\|] [\|\fB\-J\fP\|] [\|\fB\-K\fP\|] @@ -19,6 +21,7 @@ [\|\fB\-R\fP\ \fIN\fP\|] [\|\fB\-S\fP\ \fIN\fP\|] [\|\fB\-T\fP\|] +[\|\fB\-U\fP\|] [\|\fB\-X\fP\|] [\|\fB\-Y\fP\|] [\|\fB\-Z\fP\|] @@ -27,11 +30,13 @@ [\|\fB\-c\fP\|] [\|\fB\-d\fP\ \fIpath\fP\|] [\|\fB\-e\fP\|] +[\|\fB\-f\fP\ \fIstr\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-k\fP\|] [\|\fB\-l\fP\|] [\|\fB\-o\fP\ \fIfilename\fP\|] [\|\fB\-p\fP\ \fIpath\fP\|] +[\|\fB\-q\fP\|] [\|\fB\-r\fP\|] [\|\fB\-u\fP\|] [\|\fB\-v\fP\ \fIN\fP\|] @@ -54,9 +59,15 @@ \fB\-C\fP\ \fIN\fP Max count .TP +\fB\-D\fP +Disable message suppression +.TP \fB\-E\fP\ \fIstr\fP Only Error Code to Show .TP +\fB\-F\fP +Test network access +.TP \fB\-G\fP GI lookup from accession .TP @@ -116,6 +127,9 @@ \fB\-T\fP Use Threads .TP +\fB\-U\fP +Genome center submission +.TP \fB\-X\fP Exon splice check .TP @@ -131,6 +145,8 @@ .PD 0 .IP a Automatic (default) +.IP c +Catenated .IP z Any .IP e @@ -160,6 +176,9 @@ \fB\-e\fP Ignore transcription/translation Exceptions .TP +\fB\-x\fP\ \fIstr\fP +Substring filter +.TP \fB\-i\fP\ \fIfilename\fP Single input file (standard input by default) .TP @@ -175,6 +194,9 @@ \fB\-p\fP\ \fIpath\fP Path to ASN.1 Files .TP +\fB\-q\fP +Taxonomy lookup +.TP \fB\-r\fP Remote Fetching from ID .TP @@ -182,12 +204,27 @@ Recurse .TP \fB\-v\fP\ \fIN\fP -Verbosity, from \fB0\fP to \fB4\fP (\fB1\fP by default) +Verbosity: +.RS +.PD 0 +.IP 1 +Standard report (default) +.IP 2 +Accession / severity / code (space delimited) +.IP 3 +Accession / severity / code (tab delimited) +.IP 4 +XML report +.IP 5 +Accession / GI / severity / code (tab delimited) +.PD +.RE .TP \fB\-x\fP\ \fIstr\fP File selection substring (\fB.ent\fP by default) .SH AUTHOR The National Center for Biotechnology Information. .SH SEE ALSO +.BR asndisc (1), .BR cleanasn (1), .BR sequin (1). --- ncbi-tools6-6.1.20120620.orig/doc/man/blast.1 +++ ncbi-tools6-6.1.20120620/doc/man/blast.1 @@ -1,6 +1,6 @@ .TH BLAST 1 2009-08-02 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\|] @@ -34,7 +34,7 @@ .PP \" Debian renames blast to blast2 to avoid clashing with an unrelated \" blast executable. -.ds bx blast +.ds bx blast2 .B \*(bx [\|\fB\-\fP\|] [\|\fB\-B\fP\ \fIN\fP\|] --- ncbi-tools6-6.1.20120620.orig/doc/man/blast2.1 +++ ncbi-tools6-6.1.20120620/doc/man/blast2.1 @@ -0,0 +1 @@ +.so man1/blast.1 --- ncbi-tools6-6.1.20120620.orig/doc/man/cleanasn.1 +++ ncbi-tools6-6.1.20120620/doc/man/cleanasn.1 @@ -1,31 +1,41 @@ -.TH CLEANASN 1 2009-07-31 NCBI "NCBI Tools User's Manual" +.TH CLEANASN 1 2012-06-24 NCBI "NCBI Tools User's Manual" .SH NAME cleanasn \- clean up irregularities in NCBI ASN.1 objects .SH SYNOPSIS .B cleanasn [\|\fB\-\fP\|] +[\|\fB\-A\fP\ \fIfilename\fP\|] +[\|\fB\-C\fP\ \fIstr\fP\|] [\|\fB\-D\fP\ \fIstr\fP\|] [\|\fB\-F\fP\ \fIstr\fP\|] [\|\fB\-K\fP\ \fIstr\fP\|] [\|\fB\-L\fP\ \fIfilename\fP\|] [\|\fB\-M\fP\ \fIfilename\fP\|] [\|\fB\-N\fP\ \fIstr\fP\|] -[\|\fB\-P\fP\|] +[\|\fB\-P\fP\ \fIstr\fP\|] [\|\fB\-Q\fP\ \fIstr\fP\|] [\|\fB\-R\fP\|] +[\|\fB\-S\fP\ \fIstr\fP\|] [\|\fB\-T\fP\|] [\|\fB\-U\fP\ \fIstr\fP\|] +[\|\fB\-V\fP\ \fIstr\fP\|] [\|\fB\-X\fP\ \fIstr\fP\|] +[\|\fB\-Z\fP\ \fIstr\fP\|] [\|\fB\-a\fP\ \fIstr\fP\|] [\|\fB\-b\fP\|] [\|\fB\-c\fP\|] +[\|\fB\-d\fP\ \fIstr\fP\|] [\|\fB\-f\fP\ \fIstr\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] +[\|\fB\-j\fP\ \fIfilename\fP\|] +[\|\fB\-k\fP\ \fIfilename\fP\|] [\|\fB\-m\fP\ \fIstr\fP\|] +[\|\fB\-n\fP\ \fIpath\fP\|] [\|\fB\-o\fP\ \fIfilename\fP\|] [\|\fB\-p\fP\ \fIpath\fP\|] [\|\fB\-q\fP\ \fIpath\fP\|] [\|\fB\-r\fP\ \fIpath\fP\|] +[\|\fB\-v\fP\ \fIpath\fP\|] [\|\fB\-x\fP\ \fIext\fP\|] .SH DESCRIPTION \fBcleanasn\fP is a utility program to clean up irregularities in NCBI @@ -36,12 +46,40 @@ \fB\-\fP Print usage message .TP +\fB\-A\fP\ \fIfilename\fP +Accession list file +.TP +\fB\-C\fP\ \fIstr\fP +Sequence operations, per the flags in str: +.RS +.PD 0 +.IP c +Compress +.IP d +Decompress +.IP v +Virtual gaps inside segmented sequence +.IP s +Convert segmented set to delta sequence +.PD +.RE +.TP \fB\-D\fP\ \fIstr\fP Clean up descriptors, per the flags in str: .RS .PD 0 .IP t Remove Title +.IP c +Remove Comment +.IP n +Remove Nuc-Prot Set title +.IP e +Remove Pop/Phy/Mut/Eco Set title +.IP m +Remove mRNA title +.IP p +Remove Protein title .PD .RE .TP @@ -53,8 +91,16 @@ Remove User-objects .IP d Remove db_xrefs +.IP e +Remove \fB/evidence\fP and \fB/inference\fP .IP r Remove redundant gene xrefs +.IP f +Fuse duplicate features +.IP k +Package coding-region or parts features +.IP z +Delete or update EC numbers .PD .RE .TP @@ -71,9 +117,21 @@ .IP g GpipeSeqEntryCleanup .IP n -Normalize Descriptor Order +Normalize descriptor order .IP u Remove NcbiCleanup User Objects +.IP c +Synchronize genetic Codes +.IP d +Resynchronize CDS partials +.IP m +Resynchronize mRNA partials +.IP t +Resynchronize Peptide partials +.IP a +Adjust consensus splice +.IP i +Promote to "worst" Seq-ID .PD .RE .TP @@ -88,35 +146,114 @@ .RS .PD 0 .IP o -LinkCDSmRNAbyOverlap +Link CDS mRNA by Overlap .IP p -LinkCDSmRNAbyProduct +Link CDS mRNA by Product .IP r -ReassignFeatureIDs +Reassign feature IDs +.IP f +Fix missing reciprocal feature IDs .IP c -ClearFeatureIDs +Clear feature IDs .PD .RE .TP \fB\-P\fP -Publication Lookup +Publication options: +.RS +.PD 0 +.IP a +Remove All publications +.IP s +Remove Serial number +.IP f +Remove Figure, numbering, and name +.IP r +Remove Remark +.IP u +Update PMID-only publication +.IP # +Replace unpublished with PMID +.PD +.RE .TP \fB\-Q\fP\ \fIstr\fP Report: .RS .PD 0 +.IP c +Record count .IP r -ASN.1 BSEC/SSEC Report +ASN.1 BSEC report +.IP s +ASN.1 SSEC report +.IP n +NORM vs. SSEC report +.IP e +PopPhyMutEco AutoDef report +.IP o +Overlap report +.IP l +Latitude-longitude country diff +.IP d +Log SSEC differences .IP g -GenBank SSEC Diff +GenBank SSEC diff +.IP f +asn2gb/asn2flat diff +.IP h +Seg-to-delta GenBank diff +.IP v +Validator SSEC diff .IP m -Modernization +Modernize Gene/RNA/PCR +.IP u +Unpublished Pub lookup +.IP p +Published Pub lookup +.IP j +Unindexed Journal report +.IP x +Custom scan .PD .RE .TP \fB\-R\fP Remote fetching from ID (NCBI sequence databases) .TP +\fB\-S\fP\ \fIstr\fP +Selective difference filter (capital letters skip) +.RS +.PD 0 +.IP s +SSEC +.IP b +BSEC +.IP A +Author +.IP p +Publication +.IP l +Location +.IP r +RNA +.IP q +Qualifier sort order +.IP g +Genbank block +.IP k +Package CdRegion or parts features +.IP m +Move publication +.IP o +Leave duplicate Bioseq publication +.IP d +Automatic definition line +.IP e +Pop/Phy/Mut/Eco Set definition line +.PD +.RE +.TP \fB\-T\fP Taxonomy Lookup .TP @@ -133,15 +270,47 @@ .PD .RE .TP +\fB\-V\fP\ \fIstr\fP +Remove features by validator severity: +.RS +.PD 0 +.IP r +Reject +.IP e +Error +.IP w +Warning +.IP i +Info +.PD +.RE +.TP \fB\-X\fP\ \fIstr\fP Miscellaneous options, per str: .RS .PD 0 .IP d Automatic definition line +.IP e +Pop/Phy/Mut/Eco Set definition line +.IP n +Instantiate NC title +.IP m +Instantiate NM titles +.IP x +Special XM titles +.IP p +Instantiate Protein titles +.IP c +Create mRNAs for coding sequences +.IP f +Fix reciprocal protein_id/transcript_id .PD .RE .TP +\fB\-Z\fP\ \fIstr\fP +Remove indicated User-object +.TP \fB\-a\fP\ \fIstr\fP ASN.1 type .RS @@ -167,12 +336,47 @@ \fB\-c\fP Input ASN.1 is Compressed .TP +\fB\-d\fP\ \fIstr\fP +Source database +.RS +.PD 0 +.IP a +Any (default) +.IP g +GenBank +.IP e +EMBL +.IP d +DDBJ +.IP b +EMBL or DDBJ +.IP r +RefSeq +.IP n +NCBI +.IP v +Only segmented sequences +.IP w +Exclude segmented sequences +.IP x +Exclude EMBL/DDBJ +.IP y +Exclude gbcon, gbest, gbgss, gbhtg, gbpat, gbsts +.PD +.RE +.TP \fB\-f\fP\ \fIstr\fP Substring filter .TP \fB\-i\fP\ \fIfilename\fP Single input file (defaults to stdin) .TP +\fB\-j\fP\ \fIfilename\fP +First filename +.TP +\fB\-k\fP\ \fIfilename\fP +Last filename +.TP \fB\-m\fP\ \fIstr\fP Flatfile mode: .RS @@ -188,6 +392,9 @@ .PD .RE .TP +\fB\-n\fP\ \fIpath\fP +\fBasn2flat\fP executable (default is \fB/netopt/ncbi_tools/bin/asn2flat\fP) +.TP \fB\-o\fP\ \fIfilename\fP Single output file (defaults to stdout) .TP @@ -195,15 +402,19 @@ Process all matching files in \fIpath\fP .TP \fB\-q\fP\ \fIpath\fP -Ffdiff executable (default is /netopt/genbank/subtool/bin/ffdiff) +\fBffdiff\fP executable (default is \fB/netopt/genbank/subtool/bin/ffdiff\fP) .TP \fB\-r\fP\ \fIpath\fP Path for results .TP +\fB\-v\fP\ \fIpath\fP +\fBasnval\fP executable (default is \fB/netopt/ncbi_tools/bin/asnval\fP) +.TP \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). +.BR asndisc (1), +.BR asnval (1), +.BR sequin (1). --- ncbi-tools6-6.1.20120620.orig/doc/man/idfetch.1 +++ ncbi-tools6-6.1.20120620/doc/man/idfetch.1 @@ -1,4 +1,4 @@ -.TH IDFETCH 1 2007-10-19 NCBI "NCBI Tools User's Manual" +.TH IDFETCH 1 2011-09-02 NCBI "NCBI Tools User's Manual" .SH NAME idfetch \- retrieve biological data from the NCBI ID1 server .SH SYNOPSIS @@ -152,6 +152,8 @@ quality scores (Seq-entry only) .IP 7 Entrez DocSums +.IP 8 +FASTA reverse complement .PD .RE .SH AUTHOR --- ncbi-tools6-6.1.20120620.orig/doc/man/nps2gps.1 +++ ncbi-tools6-6.1.20120620/doc/man/nps2gps.1 @@ -1,4 +1,4 @@ -.TH NPS2GPS 1 2008-12-13 NCBI "NCBI Tools User's Manual" +.TH NPS2GPS 1 2012-06-24 "NCBI Tools User's Manual" .SH NAME nps2gps \- convert nucleotide-protein sets to ASN.1 genomic product sets .SH SYNOPSIS @@ -6,9 +6,14 @@ [\|\fB\-\fP\|] [\|\fB\-D\fP\|] [\|\fB\-F\fP\|] +[\|\fB\-G\fP\ \fIstr\fP\|] [\|\fB\-L\fP\|] +[\|\fB\-N\fP\|] [\|\fB\-P\fP\|] +[\|\fB\-Q\fP\|] [\|\fB\-R\fP\|] +[\|\fB\-T\fP\|] +[\|\fB\-U\fP\|] [\|\fB\-f\fP\ \fIstr\fP\|] [\|\fB\-i\fP\ \fIfilename\fP\|] [\|\fB\-o\fP\ \fIfilename\fP\|] @@ -31,15 +36,30 @@ \fB\-F\fP Map by Feature ID .TP +\fB\-G\fP\ \fIstr\fP +General ID database name +.TP \fB\-L\fP Lock components in advance .TP +\fB\-N\fP +Promote Non-coding RNAs +.TP \fB\-P\fP mRNA ID from Protein .TP +\fB\-Q\fP +Special mRNA titles +.TP \fB\-R\fP Enable Remote fetching from ID .TP +\fB\-T\fP +Map by Transcript ID +.TP +\fB\-U\fP +Remove Unnecessary gene cross-references +.TP \fB\-f\fP\ \fIstr\fP Substring filter .TP --- ncbi-tools6-6.1.20120620.orig/doc/man/sbtedit.1 +++ ncbi-tools6-6.1.20120620/doc/man/sbtedit.1 @@ -4,12 +4,12 @@ .SH SYNOPSIS .B sbtedit .SH DESCRIPTION -\fBPsbtedit\fP is a graphical editor for GenBank submission templates, -which \fBPsequin\fP(1) and \fBPtbl2asn(1)\fP can combine with +\fBsbtedit\fP is a graphical editor for GenBank submission templates, +which \fBPsequin\fP(1) and \fBtbl2asn\fP(1) can combine with sequence-specific data to produce complete submissions. .SH AUTHOR The National Center for Biotechnology Information. .SH SEE ALSO .ad l -.BR sequin (1), +.BR Psequin (1), .BR tbl2asn (1). --- ncbi-tools6-6.1.20120620.orig/doc/man/tbl2asn.1 +++ ncbi-tools6-6.1.20120620/doc/man/tbl2asn.1 @@ -1,4 +1,4 @@ -.TH TBL2ASN 1 2009-07-31 NCBI "NCBI Tools User's Manual" +.TH TBL2ASN 1 2012-06-24 NCBI "NCBI Tools User's Manual" .SH NAME tbl2asn \- prepare a GenBank submission using an ASCII feature table .SH SYNOPSIS @@ -11,11 +11,14 @@ [\|\fB\-F\fP\ \fIstr\fP\|] [\|\fB\-G\fP\ \fIstr\fP\|] [\|\fB\-H\fP\ \fIstr\fP\|] +[\|\fB\-J\fP\|] [\|\fB\-K\fP\|] [\|\fB\-L\fP\|] +[\|\fB\-M\fP\ \fIstr\fP\|] +[\|\fB\-N\fP\ \fIn\fP\|] [\|\fB\-O\fP\|] [\|\fB\-P\fP\|] -[\|\fB\-Q\fP\|] +[\|\fB\-Q\fP\ \fIstr\fP\|] [\|\fB\-R\fP\|] [\|\fB\-S\fP\|] [\|\fB\-T\fP\|] @@ -43,6 +46,7 @@ [\|\fB\-t\fP\ \fIfilename\fP\|] [\|\fB\-u\fP\|] [\|\fB\-v\fP\|] +[\|\fB\-w\fP\ \fIfilename\fP\|] [\|\fB\-x\fP\ \fIstr\fP\|] [\|\fB\-y\fP\ \fIstr\fP\|] [\|\fB\-z\fP\|] @@ -92,12 +96,33 @@ .PD .RE .TP +\fB\-J\fP +Delayed genomic product set +.TP \fB\-K\fP Safe Bioseq-set .TP \fB\-L\fP Force Local protein_id/transcript_id .TP +\fB\-M\fP\ \fIstr\fP +Master genome flags: +.RS +.PD 0 +.IP n +Normal +.IP b +Big sequence +.IP p +Power option +.IP t +TSA +.PD +.RE +.TP +\fB\-N\fP\ \fIn\fP +Project version number +.TP \fB\-O\fP Allow run-on ORFs .TP @@ -105,7 +130,15 @@ Remote publication lookup .TP \fB\-Q\fP +mRNA title policy +.RS +.PD 0 +.IP s Special mRNA titles +.IP r +RefSeq mRNA titles +.PD +.RE .TP \fB\-R\fP Remote sequence record fetching from ID @@ -127,10 +160,14 @@ Validate with Normal Stringency .IP r Validate without Country Check +.IP c +BarCode validation .IP b Generate GenBank Flatfile .IP g Generate Gene Report +.IP t +Validate with TSA check .PD .RE .TP @@ -141,8 +178,12 @@ Extra flags (combine any of the following letters) .RS .PD 0 +.IP A +Automatic definition line generation .IP C -Apply comments in \fB.cmt\fP files to all sequences +Apply Comments in \fB.cmt\fP files to all sequences +.IP E +Treat like Eukarypota in the discrepancy report .PD .RE .TP @@ -162,19 +203,26 @@ Runs of 20+ Ns are gaps, 100 Ns are unknown length .IP r20k Runs of 20+ Ns are gaps, 100 Ns are known length +.IP r10u +Runs of 10+ Ns are gaps, 100 Ns are unknown length +.IP r10k +Runs of 10+ Ns are gaps, 100 Ns are known length .IP s FASTA Set (\fBs\fP Batch, \fBs1\fP Pop, \fBs2\fP Phy, \fBs3\fP Mut, -\fBs4\fP Eco) +\fBs4\fP Eco, \fBs9\fP Small-genome) .IP d FASTA Delta .IP di FASTA Delta with Implicit Gaps .IP l -FASTA+Gap Alignment +FASTA+Gap Alignment (\fBl\fP Batch, \fBl1\fP Pop, \fBl2\fP Phy, \fBl3\fP Mut, +\fBl4\fP Eco, \fBl9\fP Small-genome) .IP z FASTA with Gap Lines .IP e PHRAP/ACE +.IP b +ASN.1 (in conjunction with \bF-M\fP) .PD .RE .TP @@ -195,6 +243,10 @@ .IP x Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends +.IP s +Add exception to short introns +.IP f +Fix product names .PD .RE .TP @@ -255,6 +307,9 @@ \fB\-v\fP Validate (deprecated in favor of \fB-V v\fP) .TP +\fB\-w\fP\ \fIfilename\fP +Single structured comment file +.TP \fB\-x\fP\ \fIstr\fP Suffix (default = \fB.fsa\fP) .TP --- ncbi-tools6-6.1.20120620.orig/make/makeall.unx +++ ncbi-tools6-6.1.20120620/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 6.310 2012/03/08 23:03:59 ucko 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 macrodlg.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 @@ -388,7 +388,7 @@ 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 macrodlg.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 @@ -486,14 +486,14 @@ 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 : $(SRCALL) ## To clean out the directory without removing make ## clean : - -rm -f *.[acho] + -rm -f *.[acho] *.glo .NO_PARALLEL: copy $(ULIB4) $(ULIB30) @@ -649,10 +649,12 @@ 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 @@ -782,7 +784,7 @@ 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-tools6-6.1.20120620.orig/make/makedemo.unx +++ ncbi-tools6-6.1.20120620/make/makedemo.unx @@ -1,4 +1,4 @@ -# makefile for demo programs +# -*- makefile -*- for demo programs # # $Id: makedemo.unx,v 6.94 2008/07/29 19:42:43 ucko Exp $ # @@ -171,22 +171,22 @@ # getmesh getmesh : getmesh.c - $(CC) -o getmesh $(LDFLAGS) getmesh.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o getmesh $(LDFLAGS) getmesh.c $(LIB1) # indexpub indexpub : indexpub.c - $(CC) -o indexpub $(LDFLAGS) indexpub.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o indexpub $(LDFLAGS) indexpub.c $(LIB1) # makeset makeset : makeset.c - $(CC) -o makeset $(LDFLAGS) makeset.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o makeset $(LDFLAGS) makeset.c $(LIB1) # getpub getpub : getpub.c - $(CC) -o getpub $(LDFLAGS) getpub.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o getpub $(LDFLAGS) getpub.c $(LIB1) # testobj @@ -207,17 +207,17 @@ # checksub checksub : checksub.c - $(CC) -o checksub $(LDFLAGS) checksub.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o checksub $(LDFLAGS) checksub.c $(LIB2) $(LIB1) # asn2ff asn2ff : asn2ff.c - $(CC) -o asn2ff $(LDFLAGS) asn2ff.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o asn2ff $(LDFLAGS) asn2ff.c $(LIB2) $(LIB1) # fa2htgs fa2htgs : fa2htgs.c - $(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) # cdscan @@ -227,19 +227,19 @@ # findspl findspl : findspl.c - $(CC) -o findspl $(LDFLAGS) findspl.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o findspl $(LDFLAGS) findspl.c $(LIB5) $(LIB2) $(LIB1) # errhdr errhdr : errhdr.c - $(CC) -o errhdr $(LDFLAGS) errhdr.c $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o errhdr $(LDFLAGS) errhdr.c $(LIB1) # asndhuff asndhuff : asndhuff.c - $(CC) -o asndhuff $(LDFLAGS) asndhuff.c $(LIB4) $(ENTREZLIBS) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o asndhuff $(LDFLAGS) asndhuff.c $(LIB3) $(LIB2) $(LIB1) # entrcmd @@ -260,59 +260,68 @@ # fastacmd fastacmd : fastacmd.c - $(CC) -o fastacmd $(LDFLAGS) fastacmd.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o fastacmd $(LDFLAGS) fastacmd.c $(LIB23) $(LIB1) # formatdb formatdb : formatdb.c - $(CC) -o formatdb $(LDFLAGS) formatdb.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o formatdb $(LDFLAGS) formatdb.c $(LIB23) $(LIB2) $(LIB1) # formatrpsdb formatrpsdb : formatrpsdb.c - $(CC) -o formatrpsdb $(LDFLAGS) formatrpsdb.c $(LIB61) $(LIB23) \ - $(LIBCOMPADJ) $(LIB60) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o formatrpsdb $(LDFLAGS) formatrpsdb.c $(LIB23) \ + $(LIB60) $(LIB2) $(LIB1) + +# blast (reincarnation of blastall from algo/blast sources) + +blast : blast_driver.c + $(CC) -o blast $(LDFLAGS) blast_driver.c $(THREAD_OBJ) $(LIB61) \ + $(LIB60) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) debruijn : debruijn.c - $(CC) -o debruijn $(LDFLAGS) debruijn.c $(LIB60) $(LIBCOMPADJ) $(LIB1) $(OTHERLIBS) + $(CC) -o debruijn $(LDFLAGS) debruijn.c $(LIB60) $(LIB1) # blastall blastall : blastall.c $(THREAD_OBJ) $(CC) -o blastall $(LDFLAGS) blastall.c $(THREAD_OBJ) $(LIB61) \ - $(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \ - $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB60) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) + +# blastall_old (version of blastall that does not link in new algo/blast libs). + +blastall_old : blastall.c $(THREAD_OBJ) + $(CC) -o blastall_old $(LDFLAGS) -DBLASTALL_TOOLS_ONLY blastall.c \ + $(THREAD_OBJ) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # blastpgp blastpgp : blastpgp.c $(THREAD_OBJ) $(CC) -o blastpgp $(LDFLAGS) blastpgp.c $(THREAD_OBJ) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # seedtop seedtop : seedtop.c $(THREAD_OBJ) $(CC) -o seedtop $(LDFLAGS) seedtop.c $(THREAD_OBJ) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # makemat makemat : makemat.c $(THREAD_OBJ) $(CC) -o makemat $(LDFLAGS) makemat.c $(THREAD_OBJ) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # copymat copymat : copymat.c $(THREAD_OBJ) $(CC) -o copymat $(LDFLAGS) copymat.c $(THREAD_OBJ) $(LIB60) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB1) $(THREAD_OTHERLIBS) # impala impala : profiles.c $(THREAD_OBJ) $(CC) -o impala $(LDFLAGS) profiles.c $(THREAD_OBJ) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) # testgen @@ -333,55 +342,51 @@ megablast : megablast.c $(THREAD_OBJ) $(CC) -o megablast $(LDFLAGS) megablast.c $(THREAD_OBJ) $(LIB61) \ - $(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) \ - $(THREAD_OTHERLIBS) + $(LIB60) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # vecscreen vecscreen : vecscreen.c $(THREAD_OBJ) $(CC) -o vecscreen $(LDFLAGS) vecscreen.c $(THREAD_OBJ) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # gil2bin gil2bin : gil2bin.c - $(CC) -o gil2bin $(LDFLAGS) gil2bin.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o gil2bin $(LDFLAGS) gil2bin.c $(LIB23) $(LIB1) # asn2idx asn2idx : asn2idx.c - $(CC) -o asn2idx $(LDFLAGS) asn2idx.c $(LIB23) $(LIBCOMPADJ) $(LIB2) \ - $(LIB1) $(OTHERLIBS) + $(CC) -o asn2idx $(LDFLAGS) asn2idx.c $(LIB2) $(LIB1) # sortbyquote sortbyquote : sortbyquote.c - $(CC) -o sortbyquote $(LDFLAGS) sortbyquote.c $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o sortbyquote $(LDFLAGS) sortbyquote.c $(LIB1) # subfuse subfuse : subfuse.c - $(CC) -o subfuse $(LDFLAGS) subfuse.c $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o subfuse $(LDFLAGS) subfuse.c $(LIB2) $(LIB1) # blastclust blastclust : blastclust.c $(THREAD_OBJ) $(CC) -o blastclust $(LDFLAGS) blastclust.c $(THREAD_OBJ) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # rpsblast rpsblast : rpsblast.c $(THREAD_OBJ) $(CC) -o rpsblast $(LDFLAGS) rpsblast.c $(THREAD_OBJ) $(LIB61) \ - $(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) \ - $(THREAD_OTHERLIBS) + $(LIB60) $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # asn2xml asn2xml : asn2xml.c $(THREAD_OBJ) - $(CC) -o asn2xml $(LDFLAGS) asn2xml.c $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o asn2xml $(LDFLAGS) asn2xml.c $(LIB2) $(LIB1) # regexp demos --- ncbi-tools6-6.1.20120620.orig/make/makenet.unx +++ ncbi-tools6-6.1.20120620/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 6.246 2011/04/26 15:32:34 ucko Exp $ # test, ignore @@ -323,6 +323,8 @@ # objects & sources needed for versions of network demo programs +OBJCN3D = cn3dmain.o + OBJDDV = ddvmain.o OBJUDV = udvmain.o @@ -438,10 +440,12 @@ 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 @@ -511,7 +515,7 @@ $(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/*.* . @@ -930,17 +934,18 @@ ## +Cn3D : $(OBJCN3D) $(BENTREZLIBS) netentcf $(BLIB36) + $(CC) -o Cn3D $(LDFLAGS) $(OBJCN3D) $(LIB31) $(LIB3000) $(LIB20) \ + $(LIB45) $(LIB22) $(LIB8) $(LIB7) \ + $(LIB400) $(LIB2) $(LIB1) $(VIBLIBS) $(OGLLIBS) + ddv : $(OBJDDV) - $(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ - $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \ - $(LIBCOMPADJ) $(LIB2) $(LIB1) \ - $(VIBLIBS) $(OTHERLIBS) + $(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB31) $(LIB20) $(LIB45) \ + $(LIB8) $(LIB7) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) udv : $(OBJUDV) - $(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ - $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \ - $(LIB23) $(LIBCOMPADJ) $(LIB2) \ - $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB31) $(LIB20) \ + $(LIB8) $(LIB7) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) Nentrez : entrez.c $(ULIB31) $(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ @@ -986,8 +991,7 @@ # asn2gb program (asn2gb) asn2gb : asn2gb.c - $(CC) -g -o asn2gb $(LDFLAGS) asn2gb.c $(LIB41) $(NETCLILIB) \ - $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o asn2gb $(LDFLAGS) asn2gb.c $(LIB23) $(LIB2) $(LIB1) # asn2gb_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable # should be used only internally within NCBI. @@ -998,9 +1002,8 @@ # asn2fsa program (asn2fsa) asn2fsa : asn2fsa.c - $(CC) -g -o asn2fsa $(LDFLAGS) asn2fsa.c $(THREAD_OBJ) $(LIB41) \ - $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \ - $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(CC) -g -o asn2fsa $(LDFLAGS) asn2fsa.c $(THREAD_OBJ) \ + $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # asn2fsa_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable # should be used only internally within NCBI. @@ -1011,14 +1014,12 @@ # asn2all program (asn2all) asn2all : asn2all.c - $(CC) -g -o asn2all $(LDFLAGS) asn2all.c $(THREAD_OBJ) $(LIB41) \ - $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \ - $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(CC) -g -o asn2all $(LDFLAGS) asn2all.c $(THREAD_OBJ) $(LIB2) $(LIB1) \ + $(THREAD_OTHERLIBS) # tbl2asn tbl2asn : tbl2asn.c - $(CC) -o tbl2asn $(LDFLAGS) tbl2asn.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS) + $(CC) -o tbl2asn $(LDFLAGS) tbl2asn.c $(LIB23) $(LIB2) $(LIB1) # tbl2asn_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable # should be used only internally within NCBI. @@ -1034,13 +1035,12 @@ # gene2xml program (gene2xml) gene2xml : gene2xml.c - $(CC) -g -o gene2xml $(LDFLAGS) gene2xml.c $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o gene2xml $(LDFLAGS) gene2xml.c $(LIB2) $(LIB1) # asnval program (asnval) asnval : asnval.c - $(CC) -g -o asnval $(LDFLAGS) asnval.c $(THREAD_OBJ) $(LIB41) \ - $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \ - $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(CC) -g -o asnval $(LDFLAGS) asnval.c $(THREAD_OBJ) $(LIB2) $(LIB1) \ + $(THREAD_OTHERLIBS) # asnval_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable # should be used only internally within NCBI. @@ -1059,8 +1059,7 @@ # asndisc program (asndisc) asndisc : asndisc.c $(CC) -g -o asndisc $(LDFLAGS) asndisc.c $(THREAD_OBJ) $(LIB41) \ - $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \ - $(OTHERLIBS) $(THREAD_OTHERLIBS) + $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS) # asndisc_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable # should be used only internally within NCBI. @@ -1083,8 +1082,8 @@ # asnmacro asnmacro : asnmacro.c - $(CC) -o asnmacro $(LDFLAGS) asnmacro.c $(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o asnmacro $(LDFLAGS) asnmacro.c $(LIB61) $(LIB60) $(LIB23) \ + $(LIB2) $(LIB1) # asnstrip program (asnstrip) asnstrip : asnstrip.c @@ -1108,28 +1107,23 @@ # gbseqget program (gbseqget) gbseqget : gbseqget.c - $(CC) -g -o gbseqget $(LDFLAGS) gbseqget.c $(LIB41) $(NETCLILIB) \ - $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o gbseqget $(LDFLAGS) gbseqget.c $(LIB2) $(LIB1) # insdseqget program (insdseqget) insdseqget : insdseqget.c - $(CC) -g -o insdseqget $(LDFLAGS) insdseqget.c $(LIB41) $(NETCLILIB) \ - $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o insdseqget $(LDFLAGS) insdseqget.c $(LIB2) $(LIB1) # nps2gps program (nps2gps) nps2gps : nps2gps.c - $(CC) -g -o nps2gps $(LDFLAGS) nps2gps.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o nps2gps $(LDFLAGS) nps2gps.c $(LIB23) $(LIB2) $(LIB1) # trna2sap program (trna2sap) trna2sap : trna2sap.c - $(CC) -g -o trna2sap $(LDFLAGS) trna2sap.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o trna2sap $(LDFLAGS) trna2sap.c $(LIB2) $(LIB1) # trna2tbl program (trna2tbl) trna2tbl : trna2tbl.c - $(CC) -g -o trna2tbl $(LDFLAGS) trna2tbl.c $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o trna2tbl $(LDFLAGS) trna2tbl.c # Entrez2 service test program (testent2) testent2 : testent2.c @@ -1138,15 +1132,14 @@ # network Entrez2 application (entrez2) entrez2 : entrez2.c - $(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \ - $(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \ - $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB20) \ + $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(VIB_POST_LINK) entrez2 # demo program (spidey) spidey : spideymain.c $(CC) -o spidey $(LDFLAGS) spideymain.c $(LIB41) $(LIB23) \ - $(LIBCOMPADJ) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS) + $(LIB2) $(LIB1) # demo program dotmatrix dotmatrix : dotmain.c @@ -1174,12 +1167,12 @@ # demo program (asn2asn) asn2asn : asn2asn.c - $(CC) -o asn2asn $(LDFLAGS) asn2asn.c $(LIB41) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o asn2asn $(LDFLAGS) asn2asn.c $(LIB2) $(LIB1) # demo program (cleanasn) cleanasn : cleanasn.c - $(CC) -o cleanasn $(LDFLAGS) cleanasn.c $(LIB41) $(LIB23) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -o cleanasn $(LDFLAGS) cleanasn.c $(LIB23) $(LIB2) $(LIB1) # cleanasn_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable # should be used only internally within NCBI. @@ -1218,27 +1211,25 @@ $(CC) -g -o id0test $(LDFLAGS) id0test.c $(LIB13) $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS) idfetch: idfetch.c $(BNETCLILIB) $(BLIB41) - $(CC) -g -o idfetch $(LDFLAGS) idfetch.c $(LIB41) $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS) + $(CC) -g -o idfetch $(LDFLAGS) idfetch.c $(LIB41) $(LIB2) $(LIB1) # gapped BLAST client # blastcl3 now has the same source code as blastall but should be compiled # with -DBLAST_CS_API flag blastcl3: blastall.c $(BNETCLILIB) $(BLIB36) $(CC) -g -o blastcl3 $(LDFLAGS) -DBLAST_CS_API blastall.c \ - $(LIB61) $(LIB60) $(LIB36) $(LIB23) $(LIBCOMPADJ) \ - $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS) + $(LIB61) $(LIB60) $(LIB36) $(LIB23) $(LIB2) $(LIB1) # BLAST 2 sequences # Uses network libraries to access Entrez for retrieving sequences by gi/accession bl2seq : bl2seq.c $(CC) -o bl2seq $(LDFLAGS) bl2seq.c $(LIB61) $(LIB60) $(LIB23) \ - $(LIBCOMPADJ) $(LIB41) $(NETCLILIB) $(LIB2) $(LIB1) \ - $(OTHERLIBS) + $(LIB41) $(LIB2) $(LIB1) taxblast: taxblast_main.c $(BLIB41) $(BLIB40) $(CC) -g -o taxblast $(LDFLAGS) taxblast_main.c \ - $(LIB61) $(LIB60) $(LIB36) $(LIB41) $(LIB40) $(LIB23) $(LIBCOMPADJ) \ - $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS) + $(LIB61) $(LIB60) $(LIB36) $(LIB41) $(LIB40) $(LIB23) \ + $(LIB2) $(LIB1) $(OTHERLIBS) # test client for the suggest network service suggcli: suggcli.c $(BNETCLILIB) $(BLIB24) @@ -1250,11 +1241,11 @@ # '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 @@ -1419,9 +1410,8 @@ $(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \ $(BLIB2) $(BLIB1) $(ULIB31) $(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \ - $(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \ - $(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \ - $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(LIB31) $(LIB20) $(LIB61) $(LIB36) $(LIB23) $(LIB11) \ + $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(VIB_POST_LINK) Psequin # 'sbtedit' Submission Template Editor @@ -1431,9 +1421,7 @@ $(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \ $(BLIB2) $(BLIB1) $(ULIB31) $(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \ - $(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \ - $(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \ - $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(LIB20) $(LIB23) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(VIB_POST_LINK) sbtedit # 'streamer' Sequinesque Stream Editor --- ncbi-tools6-6.1.20120620.orig/make/makeshlb.unx +++ ncbi-tools6-6.1.20120620/make/makeshlb.unx @@ -1,4 +1,4 @@ -# +# -*- makefile -*- # # $Id: makeshlb.unx,v 6.1 1999/03/18 17:31:11 beloslyu Exp $ # @@ -12,7 +12,112 @@ 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 $(LDFLAGS) \ + $($*_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.$(so) +libblast_sysdeps = -lm +libblastapi_deps = libblast.$(so) libncbitool.$(so) libncbiobj.$(so) \ + libncbi.$(so) +libblastapi_sysdeps = -lm +libblastcompadj_sysdeps = -lm +libncbi_sysdeps = -lm +# libncbiCacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so) +libncbiNacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so) \ + libncbiobj.$(so) libncbi.$(so) +libncbiNacc_sysdeps = -lm +# libncbiacc_deps = libncbicdr.$(so) +libncbicdr_deps = libncbiobj.$(so) libncbi.$(so) +libncbiid1_deps = libncbiobj.$(so) libnetcli.$(so) libncbi.$(so) +libncbimla_deps = libncbiobj.$(so) libnetcli.$(so) libncbi.$(so) +libncbimmdb_deps = libncbiid1.$(so) libncbitool.$(so) libncbiobj.$(so) \ + libncbi.$(so) +libncbimmdb_sysdeps = -lm +libncbiobj_deps = libncbi.$(so) +libncbiobj_sysdeps = -lm +libncbitool_deps = libblastcompadj.$(so) libncbiobj.$(so) libncbi.$(so) +libncbitool_sysdeps = -lm +libncbitxc2_deps = libncbitool.$(so) libnetcli.$(so) libncbiobj.$(so) \ + libncbi.$(so) +libncbitxc2_sysdeps = -lm +libnetblast_deps = libncbitool.$(so) libnetcli.$(so) libncbiobj.$(so) \ + libncbi.$(so) +libnetcli_deps = libncbi.$(so) +# libnetentr_deps = libncbiacc.$(so) libnetcli.$(so) +libvibgif_deps = libncbi.$(so) +libvibgif_sysdeps = -lm + +libddvlib_deps = libncbidesk.$(so) libvibrantOGL.$(so) \ + libncbitool.$(so) libncbiobj.$(so) libncbi.$(so) +libncbicn3d_deps = libncbiNacc.$(so) libddvlib.$(so) libncbidesk.$(so) \ + libncbimmdb.$(so) libncbitool.$(so) libncbiobj.$(so) \ + libncbi.$(so) +libncbicn3dOGL_deps = $(libncbicn3d_deps) libvibrantOGL.$(so) +libncbicn3dOGL_sysdeps = -lm +libncbidesk_deps = libblastapi.$(so) libncbimmdb.$(so) libncbitool.$(so) \ + libvibrantOGL.$(so) libncbiobj.$(so) libncbi.$(so) +libncbidesk_sysdeps = -lm +libvibnet_deps = libncbiNacc.$(so) libncbidesk.$(so) libncbimmdb.$(so) \ + libvibrantOGL.$(so) libncbitool.$(so) \ + libncbicdr.$(so) libncbiobj.$(so) libncbi.$(so) +# libvibrant_deps = libncbi.$(so) +# libvibrant_sysdeps = $(VIBLIBS) +# for ddvcolor stuff +libvibrantOGL_deps = libncbiobj.$(so) libncbi.$(so) +libvibrantOGL_sysdeps = $(OGLLIBS) $(VIBLIBS) -lm + +# XXX - is there a way to express these programmatically? +libblast.$(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-tools6-6.1.20120620.orig/sequin/sbtedit.c +++ ncbi-tools6-6.1.20120620/sequin/sbtedit.c @@ -44,7 +44,10 @@ * ========================================================================== */ -#ifndef CODECENTER +#ifdef BUILD_DATE +static char *date_of_compilation = BUILD_DATE; +static char *time_of_compilation = BUILD_TIME; +#elif !defined(CODECENTER) static char *date_of_compilation = __DATE__; static char *time_of_compilation = __TIME__; #else --- ncbi-tools6-6.1.20120620.orig/sequin/sequin1.c +++ ncbi-tools6-6.1.20120620/sequin/sequin1.c @@ -42,7 +42,10 @@ * ========================================================================== */ -#ifndef CODECENTER +#ifdef BUILD_DATE +static char *date_of_compilation = BUILD_DATE; +static char *time_of_compilation = BUILD_TIME; +#elif !defined(CODECENTER) static char *date_of_compilation = __DATE__; static char *time_of_compilation = __TIME__; #else --- ncbi-tools6-6.1.20120620.orig/sequin/sequin7.c +++ ncbi-tools6-6.1.20120620/sequin/sequin7.c @@ -42,7 +42,10 @@ * ========================================================================== */ -#ifndef CODECENTER +#ifdef BUILD_DATE +static char *date_of_compilation = BUILD_DATE; +static char *time_of_compilation = BUILD_TIME; +#elif !defined(CODECENTER) static char *date_of_compilation = __DATE__; static char *time_of_compilation = __TIME__; #else --- ncbi-tools6-6.1.20120620.orig/sequin/streamer.c +++ ncbi-tools6-6.1.20120620/sequin/streamer.c @@ -43,7 +43,10 @@ * ========================================================================== */ -#ifndef CODECENTER +#ifdef BUILD_DATE +static char *date_of_compilation = BUILD_DATE; +static char *time_of_compilation = BUILD_TIME; +#elif !defined(CODECENTER) static char *date_of_compilation = __DATE__; static char *time_of_compilation = __TIME__; #else --- ncbi-tools6-6.1.20120620.orig/tools/readdb.c +++ ncbi-tools6-6.1.20120620/tools/readdb.c @@ -2065,7 +2065,7 @@ #include
#endif -#ifdef __linux +#ifdef __GLIBC__ /* not just __linux */ #ifndef __USE_BSD #define __USE_BSD #endif @@ -2080,7 +2080,7 @@ #define READDBBF_READY 1 #define READDBBF_DISABLE 2 -#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) +#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) || defined(__GLIBC__) #ifndef MADV_NORMAL #undef HAVE_MADVISE #endif @@ -2115,7 +2115,7 @@ #if defined(OS_UNIX_SOL) #include -#elif defined(OS_UNIX_LINUX) +#elif defined(OS_UNIX_LINUX) || defined(__GLIBC__) #include #endif typedef struct readdbbioseqfetch { @@ -2144,7 +2144,7 @@ static ReadDBFILEPtr readdb_merge_gifiles (ReadDBFILEPtr rdfp_chain); static Boolean s_IsTextFile(const char* filename); -#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) +#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) || defined(__GLIBC__) #ifdef HAVE_MADVISE static void readdb_preload_index (ReadDBFILEPtr rdfp, Int4 first_db_seq, Int4 final_db_seq, EMemMapAdvise advice, Boolean sync); @@ -4824,7 +4824,7 @@ NlmMutexUnlock(hdrseq_mutex); } -#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) +#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) || defined(__GLIBC__) #ifdef HAVE_MADVISE if( useMadvise && rdfp != NULL ) { EThreadPriority pri = eTP_Highest; @@ -12709,7 +12709,7 @@ } -#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) +#if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX) || defined(__GLIBC__) #ifdef HAVE_MADVISE /* IMPORTANT INFO: --- ncbi-tools6-6.1.20120620.orig/tools/spidey.c +++ ncbi-tools6-6.1.20120620/tools/spidey.c @@ -2088,7 +2088,7 @@ fprintf(ofp2, " "); ctr++; } - fprintf(ofp2, buf); + fwrite(buf, 1, ctr, ofp2); if (spp){ SeqPortFree(spp); } @@ -2417,7 +2417,7 @@ ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10); if (ctr > 0) buf[ctr] = '\0'; - fprintf(ofp2, buf); + fwrite(buf, 1, ctr, ofp2); SeqPortFree(spp); } done = TRUE; --- ncbi-tools6-6.1.20120620.orig/vibrant/netscape.c +++ ncbi-tools6-6.1.20120620/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); } --- ncbi-tools6-6.1.20120620.orig/vibrant/shim3d.c +++ ncbi-tools6-6.1.20120620/vibrant/shim3d.c @@ -312,6 +312,7 @@ #ifdef _PNG #include /* must go berore ncbi headers */ +#include #endif /* from ncbimisc.h */ @@ -327,7 +328,8 @@ #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 +2713,9 @@ 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 +2929,15 @@ 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; @@ -3153,8 +3166,11 @@ Message(MSG_ERROR, "Can't create PNG info structure"); goto cleanup; } - +#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >= 4 + if (setjmp(png_jmpbuf(png_ptr))) { +#else if (setjmp(png_ptr->jmpbuf)) { +#endif Message(MSG_ERROR, "PNG write failed"); goto cleanup; } @@ -3705,4 +3721,3 @@ if (fblock) MemFree(fblock); } - --- ncbi-tools6-6.1.20120620.orig/vibrant/vibmain.c +++ ncbi-tools6-6.1.20120620/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-tools6-6.1.20120620.orig/vibrant/vibwndws.c +++ ncbi-tools6-6.1.20120620/vibrant/vibwndws.c @@ -6789,7 +6789,7 @@ Nlm_InitPrompt (); Nlm_InitSlate (); Nlm_InitTexts (); - if (! Nlm_SetupWindows ()) return; + if (! Nlm_SetupWindows ()) exit(1); Nlm_RegisterWindows (); Nlm_RegisterTexts (); Nlm_RegisterSlates ();