[med-svn] [Git][med-team/cufflinks][master] 6 commits: Drop gffread binary, add gffread package to Recommends in d/control
Alexandre Mestiashvili
gitlab at salsa.debian.org
Tue Aug 20 18:06:36 BST 2019
Alexandre Mestiashvili pushed to branch master at Debian Med / cufflinks
Commits:
c0e972e4 by Alexandre Mestiashvili at 2019-08-20T15:43:54Z
Drop gffread binary, add gffread package to Recommends in d/control
- - - - -
65141d81 by Alexandre Mestiashvili at 2019-08-20T15:46:55Z
Switch to debhelper-compat, bump Policy to 4.4.0
- - - - -
c02c0373 by Alexandre Mestiashvili at 2019-08-20T15:51:02Z
Add README.Debian, explaining why gffread is removed from cufflinks
- - - - -
0711a123 by Alexandre Mestiashvili at 2019-08-20T16:05:39Z
Remove gffread_show_usage.patch from d/patches/series
- - - - -
15340b02 by Alexandre Mestiashvili at 2019-08-20T16:11:14Z
Update my email address in Uploaders in d/control
- - - - -
2a00eb81 by Alexandre Mestiashvili at 2019-08-20T16:11:25Z
Update changelog
Gbp-Dch: Ignore
- - - - -
7 changed files:
- + debian/README.Debian
- debian/changelog
- − debian/compat
- debian/control
- − debian/patches/gffread_show_usage.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,4 @@
+Since version 2.2.1+dfsg.1-4 the gffread binary is not shipped with cufflinks,
+because up-to-date gffread binary is available via gffread package.
+
+ -- Alex Mestiashvili <mestia at debian.org> Tue, 20 Aug 2019 17:37:37 +0200
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+cufflinks (2.2.1+dfsg.1-4) unstable; urgency=medium
+
+ [ Valentin Marcon ]
+ * Correct DOI
+
+ [ Alexandre Mestiashvili ]
+ * Drop gffread binary, add gffread package to Recommends in d/control
+ Closes: #934600
+ * Switch to debhelper-compat, bump Policy to 4.4.0, update Uploader's
+ email address
+ * Add README.Debian, explaining why gffread is removed from cufflinks
+
+ -- Alexandre Mestiashvili <mestia at debian.org> Tue, 20 Aug 2019 17:51:28 +0200
+
cufflinks (2.2.1+dfsg.1-3) unstable; urgency=medium
* XS-Autobuild: yes
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -1,12 +1,12 @@
Source: cufflinks
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>,
+Uploaders: Alexandre Mestiashvili <mestia at debian.org>,
Andreas Tille <tille at debian.org>,
Charles Plessy <plessy at debian.org>
Section: non-free/science
XS-Autobuild: yes
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
help2man,
libboost-dev,
libboost-serialization-dev,
@@ -16,7 +16,7 @@ Build-Depends: debhelper (>= 11~),
zlib1g-dev,
python,
libeigen3-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/cufflinks
Vcs-Git: https://salsa.debian.org/med-team/cufflinks.git
Homepage: http://cufflinks.cbcb.umd.edu
@@ -26,6 +26,7 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
python
+Recommends: gffread
Enhances: tophat
Description: Transcript assembly, differential expression and regulation for RNA-Seq
Cufflinks assembles transcripts, estimates their abundances, and tests for
=====================================
debian/patches/gffread_show_usage.patch deleted
=====================================
@@ -1,154 +0,0 @@
-From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
-Subject: fix wrong USAGE indentation causing buffer overflow in gffread when
- using -h, --help and other arguments.
-Forwarded: yes
---- cufflinks.orig/src/gffread.cpp
-+++ cufflinks/src/gffread.cpp
-@@ -12,77 +12,77 @@
- [-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\n\
- [-CTVNJMKQAFGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]\n\
- [-i <maxintron>] \n\
-- Filters and/or converts GFF3/GTF2 records.\n\
-- <input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\
-+Filters and/or converts GFF3/GTF2 records.\n\
-+<input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\
-+\n\
-+Options:\n\
-+ -g full path to a multi-fasta file with the genomic sequences\n\
-+ for all input mappings, OR a directory with single-fasta files\n\
-+ (one per genomic sequence, with file names matching sequence names)\n\
-+ -s <seq_info.fsize> is a tab-delimited file providing this info\n\
-+ for each of the mapped sequences:\n\
-+ <seq-name> <seq-length> <seq-description>\n\
-+ (useful for -A option with mRNA/EST/protein mappings)\n\
-+ -i discard transcripts having an intron larger than <maxintron>\n\
-+ -r only show transcripts overlapping coordinate range <start>..<end>\n\
-+ (on chromosome/contig <chr>, strand <strand> if provided)\n\
-+ -R for -r option, discard all transcripts that are not fully \n\
-+ contained within the given range\n\
-+ -U discard single-exon transcripts\n\
-+ -C coding only: discard mRNAs that have no CDS feature\n\
-+ -F full GFF attribute preservation (all attributes are shown)\n\
-+ -G only parse additional exon attributes from the first exon\n\
-+ and move them to the mRNA level (useful for GTF input)\n\
-+ -A use the description field from <seq_info.fsize> and add it\n\
-+ as the value for a 'descr' attribute to the GFF record\n\
- \n\
-- Options:\n\
-- -g full path to a multi-fasta file with the genomic sequences\n\
-- for all input mappings, OR a directory with single-fasta files\n\
-- (one per genomic sequence, with file names matching sequence names)\n\
-- -s <seq_info.fsize> is a tab-delimited file providing this info\n\
-- for each of the mapped sequences:\n\
-- <seq-name> <seq-length> <seq-description>\n\
-- (useful for -A option with mRNA/EST/protein mappings)\n\
-- -i discard transcripts having an intron larger than <maxintron>\n\
-- -r only show transcripts overlapping coordinate range <start>..<end>\n\
-- (on chromosome/contig <chr>, strand <strand> if provided)\n\
-- -R for -r option, discard all transcripts that are not fully \n\
-- contained within the given range\n\
-- -U discard single-exon transcripts\n\
-- -C coding only: discard mRNAs that have no CDS feature\n\
-- -F full GFF attribute preservation (all attributes are shown)\n\
-- -G only parse additional exon attributes from the first exon\n\
-- and move them to the mRNA level (useful for GTF input)\n\
-- -A use the description field from <seq_info.fsize> and add it\n\
-- as the value for a 'descr' attribute to the GFF record\n\
-- \n\
-- -O process also non-transcript GFF records (by default non-transcript\n\
-- records are ignored)\n\
-- -V discard any mRNAs with CDS having in-frame stop codons\n\
-- -H for -V option, check and adjust the starting CDS phase\n\
-- if the original phase leads to a translation with an \n\
-- in-frame stop codon\n\
-- -B for -V option, single-exon transcripts are also checked on the\n\
-- opposite strand\n\
-- -N discard multi-exon mRNAs that have any intron with a non-canonical\n\
-- splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)\n\
-- -J discard any mRNAs that either lack initial START codon\n\
-- or the terminal STOP codon, or have an in-frame stop codon\n\
-- (only print mRNAs with a fulll, valid CDS)\n\
-- --no-pseudo: filter out records matching the 'pseudo' keyword\n\
-- \n\
-- -M/--merge : cluster the input transcripts into loci, collapsing matching\n\
-- transcripts (those with the same exact introns and fully contained)\n\
-- -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n\
-- --cluster-only: same as --merge but without collapsing matching transcripts\n\
-- -K for -M option: also collapse shorter, fully contained transcripts\n\
-- with fewer introns than the container\n\
-- -Q for -M option, remove the containment restriction:\n\
-- (multi-exon transcripts will be collapsed if just their introns match,\n\
-- while single-exon transcripts can partially overlap (80%))\n\
-- \n\
-- --force-exons: make sure that the lowest level GFF features are printed as \n\
-- \"exon\" features\n\
-- -E expose (warn about) duplicate transcript IDs and other potential \n\
-- problems with the given GFF/GTF records\n\
-- -D decode url encoded characters within attributes\n\
-- -Z merge close exons into a single exon (for intron size<4)\n\
-- -w write a fasta file with spliced exons for each GFF transcript\n\
-- -x write a fasta file with spliced CDS for each GFF transcript\n\
-- -W for -w and -x options, also write for each fasta record the exon\n\
-- coordinates projected onto the spliced sequence\n\
-- -y write a protein fasta file with the translation of CDS for each record\n\
-- -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n\
-- -m <chr_replace> is a reference (genomic) sequence replacement table with\n\
-- this format:\n\
-- <original_ref_ID> <new_ref_ID>\n\
-- GFF records on reference sequences that are not found among the\n\
-- <original_ref_ID> entries in this file will be filtered out\n\
-- -o the \"filtered\" GFF records will be written to <outfile.gff>\n\
-- (use -o- for printing to stdout)\n\
-- -t use <trackname> in the second column of each GFF output line\n\
-- -T -o option will output GTF format instead of GFF3\n\
-- "
-+ -O process also non-transcript GFF records (by default non-transcript\n\
-+ records are ignored)\n\
-+ -V discard any mRNAs with CDS having in-frame stop codons\n\
-+ -H for -V option, check and adjust the starting CDS phase\n\
-+ if the original phase leads to a translation with an \n\
-+ in-frame stop codon\n\
-+ -B for -V option, single-exon transcripts are also checked on the\n\
-+ opposite strand\n\
-+ -N discard multi-exon mRNAs that have any intron with a non-canonical\n\
-+ splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)\n\
-+ -J discard any mRNAs that either lack initial START codon\n\
-+ or the terminal STOP codon, or have an in-frame stop codon\n\
-+ (only print mRNAs with a fulll, valid CDS)\n\
-+ --no-pseudo: filter out records matching the 'pseudo' keyword\n\
-+\n\
-+ -M/--merge : cluster the input transcripts into loci, collapsing matching\n\
-+ transcripts (those with the same exact introns and fully contained)\n\
-+ -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n\
-+ --cluster-only: same as --merge but without collapsing matching transcripts\n\
-+ -K for -M option: also collapse shorter, fully contained transcripts\n\
-+ with fewer introns than the container\n\
-+ -Q for -M option, remove the containment restriction:\n\
-+ (multi-exon transcripts will be collapsed if just their introns match,\n\
-+ while single-exon transcripts can partially overlap (80%))\n\
-+\n\
-+ --force-exons: make sure that the lowest level GFF features are printed as \n\
-+ \"exon\" features\n\
-+ -E expose (warn about) duplicate transcript IDs and other potential \n\
-+ problems with the given GFF/GTF records\n\
-+ -D decode url encoded characters within attributes\n\
-+ -Z merge close exons into a single exon (for intron size<4)\n\
-+ -w write a fasta file with spliced exons for each GFF transcript\n\
-+ -x write a fasta file with spliced CDS for each GFF transcript\n\
-+ -W for -w and -x options, also write for each fasta record the exon\n\
-+ coordinates projected onto the spliced sequence\n\
-+ -y write a protein fasta file with the translation of CDS for each record\n\
-+ -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n\
-+ -m <chr_replace> is a reference (genomic) sequence replacement table with\n\
-+ this format:\n\
-+ <original_ref_ID> <new_ref_ID>\n\
-+ GFF records on reference sequences that are not found among the\n\
-+ <original_ref_ID> entries in this file will be filtered out\n\
-+ -o the \"filtered\" GFF records will be written to <outfile.gff>\n\
-+ (use -o- for printing to stdout)\n\
-+ -t use <trackname> in the second column of each GFF output line\n\
-+ -T -o option will output GTF format instead of GFF3\n\
-+"
-
-
- class SeqInfo { //populated from the -s option of gffread
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,5 @@
boost1.65.patch
fix_gcc-7_ftbfs.patch
-gffread_show_usage.patch
0004-fix-m64-usage-and-lfs.patch
0001-fix_spelling.patch
0002-bam2samtools.patch
=====================================
debian/rules
=====================================
@@ -16,6 +16,11 @@ override_dh_auto_clean:
dh_auto_clean
rm -rf autom4te.cache
+override_dh_auto_install:
+ dh_auto_install
+ # skip gffread binary provided by gffread package
+ rm -rf $(bindir)/gffread
+
override_dh_installman:
dh_installman
@@ -28,7 +33,3 @@ cuffdiff cuffquant cuffnorm cufflinks ; do \
--version-string="$(DEB_VERSION)" \
$(bindir)/$$i > $(mandir)/$$i.1; \
done
- help2man --no-info --no-discard-stderr \
- --name='component of cufflinks suite' \
- --version-string="$(DEB_VERSION)" \
- $(bindir)/gffread > $(mandir)/gffread.1; \
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/compare/2ab4d8a1afd8265019af3df01ce0123f0671aa93...2a00eb8155dc507f66a97bda471e279db019663d
--
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/compare/2ab4d8a1afd8265019af3df01ce0123f0671aa93...2a00eb8155dc507f66a97bda471e279db019663d
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