diff -Nru rtax-0.984/debian/changelog rtax-0.984/debian/changelog --- rtax-0.984/debian/changelog 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/changelog 2020-05-15 05:51:45.000000000 +0000 @@ -1,3 +1,28 @@ +rtax (0.984-7) unstable; urgency=medium + + [ Dylan Aïssi ] + * Fix Maintainer + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Steffen Möller ] + * Update metadata with ref to conda + + [ 肖盛文 ] + * fix lintian: file-contains-trailing-whitespace + * fix lintian: insecure-copyright-format-uri + * New maintainer (Closes: #960138) + * add fix.perl.path.patch + * d/control: + - Bump debhelper-compat (= 13) + - Bump Standards-Version: 4.5.0 + - add Rules-Requires-Root: no + * d/watch: + - use @PACKAGE@ @ANY_VERSION@ @ARCHIVE_EXT@ + + -- xiao sheng wen Fri, 15 May 2020 13:51:45 +0800 + rtax (0.984-6) unstable; urgency=medium * Team upload. @@ -29,7 +54,7 @@ * Team upload. * Upstream author moved to github.com, updated all metadata URLs. - * Move debian/upstream to debian/upstream/metadata (Thanks to + * Move debian/upstream to debian/upstream/metadata (Thanks to James McCoy ). Removes lintian warning. -- Simon Kainz Thu, 27 Nov 2014 12:03:57 +0000 @@ -46,7 +71,7 @@ * Initial release. (Closes: #724280) * Removed broken magic to find scripts-subdir, because we know where rtax is installed (set_script_dir.path) - * Change interpreter to bash to prevent syntax + * Change interpreter to bash to prevent syntax error warnings (fix-bash-syntax-error.patch) * Added minimal manpage. diff -Nru rtax-0.984/debian/compat rtax-0.984/debian/compat --- rtax-0.984/debian/compat 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 diff -Nru rtax-0.984/debian/control rtax-0.984/debian/control --- rtax-0.984/debian/control 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/control 2020-05-15 05:29:41.000000000 +0000 @@ -1,10 +1,11 @@ Source: rtax -Maintainer: Med Packaging Team -Uploaders: Simon Kainz +Maintainer: Debian Med Packaging Team +Uploaders: xiao sheng wen Section: science Priority: optional -Build-Depends: debhelper (>= 11~) -Standards-Version: 4.1.5 +Build-Depends: debhelper-compat (= 13) +Standards-Version: 4.5.0 +Rules-Requires-Root: no Vcs-Browser: https://salsa.debian.org/med-team/rtax Vcs-Git: https://salsa.debian.org/med-team/rtax.git Homepage: https://github.com/davidsoergel/rtax/ @@ -14,7 +15,7 @@ Depends: ${misc:Depends}, ${perl:Depends} Description: Classification of sequence reads of 16S ribosomal RNA gene - Short-read technologies for microbial community profiling are increasingly - popular, yet previous techniques for assigning taxonomy to paired-end reads - perform poorly. RTAX provides rapid taxonomic assignments of paired-end + Short-read technologies for microbial community profiling are increasingly + popular, yet previous techniques for assigning taxonomy to paired-end reads + perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads using a consensus algorithm. diff -Nru rtax-0.984/debian/copyright rtax-0.984/debian/copyright --- rtax-0.984/debian/copyright 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/copyright 2020-05-15 05:22:32.000000000 +0000 @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: RTAX Upstream-Contact: David A. W. Soergel Source: https://github.com/davidsoergel/rtax diff -Nru rtax-0.984/debian/patches/fix.perl.path.patch rtax-0.984/debian/patches/fix.perl.path.patch --- rtax-0.984/debian/patches/fix.perl.path.patch 1970-01-01 00:00:00.000000000 +0000 +++ rtax-0.984/debian/patches/fix.perl.path.patch 2020-05-15 05:39:19.000000000 +0000 @@ -0,0 +1,81 @@ +Description: update perl path + . +Author: xiao sheng wen + +--- + +Origin: xiao sheng wen +Last-Update: 2020-05-15 + +--- rtax-0.984.orig/scripts/classificationQualityFilter.pl ++++ rtax-0.984/scripts/classificationQualityFilter.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + my $countThreshold = $ARGV[0]; + my $localMinProportionThreshold = $ARGV[1]; +--- rtax-0.984.orig/scripts/classificationQualityStripper.pl ++++ rtax-0.984/scripts/classificationQualityStripper.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + while () { + my $line = $_; +--- rtax-0.984.orig/scripts/fastaidx.pl ++++ rtax-0.984/scripts/fastaidx.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use strict; + use warnings; +--- rtax-0.984.orig/scripts/greengenesExtract.pl ++++ rtax-0.984/scripts/greengenesExtract.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use strict; + use warnings; +--- rtax-0.984.orig/scripts/joinDelimitedFasta.pl ++++ rtax-0.984/scripts/joinDelimitedFasta.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use strict; + use warnings; +--- rtax-0.984.orig/scripts/parseUclustClusters.pl ++++ rtax-0.984/scripts/parseUclustClusters.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + # read a uclust result file; for each query sequence, collect the prokMSAids of the hits. + +--- rtax-0.984.orig/scripts/rtaxSearch.pl ++++ rtax-0.984/scripts/rtaxSearch.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + # RTAX: Rapid and accurate taxonomic classification of short paired-end + # sequence reads from the 16S ribosomal RNA gene. +--- rtax-0.984.orig/scripts/rtaxVote.pl ++++ rtax-0.984/scripts/rtaxVote.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + # read the prokMSAids of the hits, as produced by exactMatchIds. + # Then grab the taxonomy info for those prokMSAids and make some classification info from the set. +--- rtax-0.984.orig/scripts/splitDelimitedFasta.pl ++++ rtax-0.984/scripts/splitDelimitedFasta.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use strict; + use warnings; diff -Nru rtax-0.984/debian/patches/series rtax-0.984/debian/patches/series --- rtax-0.984/debian/patches/series 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/patches/series 2020-05-15 05:37:44.000000000 +0000 @@ -1,2 +1,3 @@ fix-bash-syntax-error.patch find_script_path.patch +fix.perl.path.patch diff -Nru rtax-0.984/debian/rules rtax-0.984/debian/rules --- rtax-0.984/debian/rules 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/rules 2020-05-15 05:27:17.000000000 +0000 @@ -1,5 +1,3 @@ #!/usr/bin/make -f %: dh $@ - - diff -Nru rtax-0.984/debian/upstream/metadata rtax-0.984/debian/upstream/metadata --- rtax-0.984/debian/upstream/metadata 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/upstream/metadata 2020-05-15 04:52:48.000000000 +0000 @@ -6,20 +6,27 @@ Repository: https://github.com/davidsoergel/rtax.git Repository-Browse: https://github.com/davidsoergel/rtax Reference: - Author: David A W Soergel and Neelendu Dey and Rob Knight and Steven E Brenner - Title: Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences - Journal: The ISME Journal - Year: 2012 - Volume: 6 - Pages: 1440–1444 - DOI: 10.1038/ismej.2011.208 - PMID: 22237546 - URL: http://www.nature.com/ismej/journal/v6/n7/abs/ismej2011208a.html - eprint: http://www.nature.com/ismej/journal/v6/n7/pdf/ismej2011208a.pdf + - Author: > + David A. W. Soergel and Neelendu Dey and Rob Knight and Steven E. Brenner + Title: > + Selection of primers for optimal taxonomic classification of + environmental 16S rRNA gene sequences + Journal: The ISME Journal + Year: 2012 + Volume: 6 + Pages: 1440–1444 + DOI: 10.1038/ismej.2011.208 + PMID: 22237546 + URL: http://www.nature.com/ismej/journal/v6/n7/abs/ismej2011208a.html + eprint: http://www.nature.com/ismej/journal/v6/n7/pdf/ismej2011208a.pdf Registry: - - Name: OMICtools - Entry: OMICS_28979 - - Name: SciCrunch - Entry: NA - - Name: bio.tools - Entry: NA + - Name: OMICtools + Entry: OMICS_28979 + - Name: SciCrunch + Entry: NA + - Name: bio.tools + Entry: NA + - Name: conda:bioconda + Entry: NA + - Name: conda:conda-forge + Entry: NA \ No newline at end of file diff -Nru rtax-0.984/debian/watch rtax-0.984/debian/watch --- rtax-0.984/debian/watch 2018-07-18 19:36:09.000000000 +0000 +++ rtax-0.984/debian/watch 2020-05-15 05:50:01.000000000 +0000 @@ -1,3 +1,3 @@ version=4 -https://github.com/davidsoergel/rtax .*davidsoergel.com/rtax-(\d[.\d]+)\.tgz +https://github.com/davidsoergel/@PACKAGE@ .*davidsoergel.com/@PACKAGE@@ANY_VERSION@@ARCHIVE_EXT@