* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/
@ 2015-04-30 22:48 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-04-30 22:48 UTC (permalink / raw
To: gentoo-commits
commit: cb4121a23d10b5a0879682b261c0e55e483bc218
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 22:46:00 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 22:46:00 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb4121a2
sci-biology/TransDecoder: renamed package to keep original letter-casing
Package-Manager: portage-2.2.18
sci-biology/TransDecoder/ChangeLog | 54 ++++++++
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 69 +++++++++++
sci-biology/TransDecoder/files/TransDecoder.patch | 136 +++++++++++++++++++++
.../TransDecoder/files/pfam_runner.pl.patch | 20 +++
sci-biology/TransDecoder/metadata.xml | 9 ++
5 files changed, 288 insertions(+)
diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog
new file mode 100644
index 0000000..6fd8f5c
--- /dev/null
+++ b/sci-biology/TransDecoder/ChangeLog
@@ -0,0 +1,54 @@
+# ChangeLog for sci-biology/transdecoder
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: more ebuild cleanup
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: ebuild cleanup
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: drop old
+
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: fixed installation of perl-related files
+
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild:
+ dropped hmmer dependency altogether, added pkg_postinst() with
+ usage/dependency info
+
+*transdecoder-2.0.1 (19 Mar 2015)
+
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
+ removing KEYWORDS until the perl files are installed to some other place. At
+ the moment I get: 'perl-module.eclass: Suspicious environment values found.
+ PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/TransDecoder"'
+
+ 15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-20140704.ebuild:
+ drop hmmer-3 dependency, it is an optional dependency only
+
+ 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-20140704.ebuild:
+ install *.pm into PERL5LIB/TransDecoder and pass that via env.d
+
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/TransDecoder.patch, +files/pfam_runner.pl.patch,
+ transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: added patches so that we use PATH to loclate
+ binaries and not in a local subdirectory named 'util', drop sys-
+ cluster/openmpi requirement, it does not link against it all all, this is a
+ bunch of perl and shell scripts
+
+*transdecoder-20140704 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: new package
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
new file mode 100644
index 0000000..e8f5134
--- /dev/null
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
+HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
+SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/cd-hit
+ sci-biology/hmmer
+ sci-biology/parafly
+ sci-biology/ffindex"
+# cdhit-4.6.1 is a real dependency, at least hmmer is optional (also ncbi-tools++ is now used for ORF searches)
+
+S="${WORKDIR}"/TransDecoder-2.0.1
+
+##src_prepare(){
+# #mv Makefile Makefile.old
+# #epatch "${FILESDIR}"/TransDecoder.patch
+# #epatch "${FILESDIR}"/pfam_runner.pl.patch
+#}
+
+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
+#
+# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+
+src_install(){
+ dobin TransDecoder.Predict TransDecoder.LongOrfs
+ insinto /usr/share/${PN}/util
+ dobin util/*.pl
+ # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
+ rm -rf util/bin
+ #
+ # * sci-biology/trinityrnaseq-20140413:0::science
+ # * /usr/bin/Fasta_reader.pm
+ # * /usr/bin/GFF3_utils.pm
+ # * /usr/bin/Gene_obj.pm
+ # * /usr/bin/Gene_obj_indexer.pm
+ # * /usr/bin/Longest_orf.pm
+ # * /usr/bin/Nuc_translator.pm
+ # * /usr/bin/TiedHash.pm
+ #
+ perl_set_version
+ insinto ${VENDOR_LIB}/${PN}
+ dobin PerlLib/*.pm # BUG: install into /usr/bin but wanted to have it readable and executable in ${VENDOR_LIB}/${PN} instead
+ einfo "Fetch on your own:"
+ einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
+ einfo "hmmpress Pfam-AB.hmm.bin"
+}
+
+pkg_postinst(){
+ einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast"
+ einfo "from either sci-biology/ncbi-blast+ (released more often) or"
+ einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)"
+ einfo "Author says the minimum requirement is sci-biology/cd-hit"
+}
diff --git a/sci-biology/TransDecoder/files/TransDecoder.patch b/sci-biology/TransDecoder/files/TransDecoder.patch
new file mode 100644
index 0000000..c0cff94
--- /dev/null
+++ b/sci-biology/TransDecoder/files/TransDecoder.patch
@@ -0,0 +1,136 @@
+--- /usr/bin/TransDecoder 2015-01-09 11:22:55.000000000 +0100
++++ TransDecoder 2015-01-09 14:31:44.095839522 +0100
+@@ -48,7 +48,7 @@
+ --prepare_pfam Prepare data for PFAM search and then quit (for running PFAM on HPC/computing cluster
+ with or without MPI )
+
+- --CPU <int> number of threads to use; (default: 2)
++ --CPU <int> number of threads to use; (default: 1)
+
+ --MPI use MPI w/ execution of hmmscan
+
+@@ -76,7 +76,7 @@
+
+ =head1 PFAM
+
+-You will need hmmer installed. Use hmmpress to prepare the database for hmmer.
++You will need hmmer installed. Use hmmpress from >=hmmer-3.0 to prepare the database for hmmer.
+ L<See|https://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin> for downloading the database.
+
+ =head1 CD-HIT
+@@ -105,7 +105,6 @@
+ use Longest_orf;
+
+ my $UTIL_DIR = "$FindBin::RealBin/util";
+-$ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+ $ENV{LD_LIBRARY_PATH} .= ":$FindBin::RealBin/util/lib64";
+
+ my ($cd_hit_est_exec) = &check_program('cd-hit-est');
+@@ -124,7 +123,7 @@
+ my $verbose;
+ my $search_pfam = "";
+ my ($reuse,$pfam_out);
+-my $CPU = 2;
++my $CPU = 1;
+ my $RETAIN_LONG_ORFS = 900;
+ my $MPI = 0;
+
+@@ -330,15 +329,15 @@
+ my $top_cds_file = $train_file && -s $train_file ? $train_file : "$cds_file.top_${top_ORFs_train}_longest";
+ if (!-s $top_cds_file) {
+ # get longest entries
+- my $cmd = "$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train > $top_cds_file";
++ my $cmd = "get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train > $top_cds_file";
+
+ unless ($reuse && -s $top_cds_file){
+ if ($cd_hit_est_exec){
+ # to speed things up only check for redundancy up to 4x the number of entries we want
+ my $red_num = $top_ORFs_train * 4 ;
+- &process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file $red_num > $workdir/redundant_top");
++ &process_cmd("get_top_longest_fasta_entries.pl $cds_file $red_num > $workdir/redundant_top");
+ &process_cmd("$cd_hit_est_exec -r 1 -i $workdir/redundant_top -o $workdir/redundant_top.nr90 -M 0 -T $CPU >/dev/null 2>/dev/null");
+- &process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl $workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
++ &process_cmd("get_top_longest_fasta_entries.pl $workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
+ unlink("$workdir/redundant_top");
+ unlink("$workdir/redundant_top.nr90");
+ unlink("$workdir/redundant_top.nr90.bak.clstr");
+@@ -349,20 +348,20 @@
+ }
+ }
+
+-$cmd = "$UTIL_DIR/compute_base_probs.pl $transcripts_file $TOP_STRAND_ONLY > $workdir/base_freqs.dat";
++$cmd = "compute_base_probs.pl $transcripts_file $TOP_STRAND_ONLY > $workdir/base_freqs.dat";
+ &process_cmd($cmd) unless $reuse && -s "$workdir/base_freqs.dat";
+
+
+ # get hexamer scores
+-#$cmd = "$UTIL_DIR/seq_n_background_to_logliklihood_vals.pl $top_cds_file $transcripts_file.random > hexamer.scores";
++#$cmd = "seq_n_background_to_logliklihood_vals.pl $top_cds_file $transcripts_file.random > hexamer.scores";
+ #&process_cmd($cmd) unless ($reuse && -s "hexamer.scores");
+
+-$cmd = "$UTIL_DIR/seq_n_baseprobs_to_logliklihood_vals.pl $top_cds_file $workdir/base_freqs.dat > $workdir/hexamer.scores";
++$cmd = "seq_n_baseprobs_to_logliklihood_vals.pl $top_cds_file $workdir/base_freqs.dat > $workdir/hexamer.scores";
+ &process_cmd($cmd) unless $reuse && -s "$workdir/hexamer.scores";
+
+
+ # score all cds entries
+-$cmd = "$UTIL_DIR/score_CDS_liklihood_all_6_frames.pl $cds_file $workdir/hexamer.scores > $cds_file.scores";
++$cmd = "score_CDS_liklihood_all_6_frames.pl $cds_file $workdir/hexamer.scores > $cds_file.scores";
+ &process_cmd($cmd) unless ($reuse && -s "$cds_file.scores");
+
+
+@@ -440,18 +439,18 @@
+ }
+
+ # index the current gff file:
+-$cmd = "$UTIL_DIR/index_gff3_files_by_isoform.pl $gff3_file";
++$cmd = "index_gff3_files_by_isoform.pl $gff3_file";
+ &process_cmd($cmd);
+
+ # retrieve the best entries:
+-$cmd = "$UTIL_DIR/gene_list_to_gff.pl $acc_file $gff3_file.inx > $cds_file.best_candidates.gff3";
++$cmd = "gene_list_to_gff.pl $acc_file $gff3_file.inx > $cds_file.best_candidates.gff3";
+ &process_cmd($cmd);
+
+ {
+ my $final_output_prefix = basename($transcripts_file) . ".transdecoder";
+
+ # exclude shadow orfs (smaller orfs in different reading frame that are eclipsed by longer orfs)
+- $cmd = "$UTIL_DIR/remove_eclipsed_ORFs.pl $cds_file.best_candidates.gff3 > $final_output_prefix.gff3";
++ $cmd = "remove_eclipsed_ORFs.pl $cds_file.best_candidates.gff3 > $final_output_prefix.gff3";
+ &process_cmd($cmd);
+
+
+@@ -462,14 +461,14 @@
+ my $gff3_file = "$final_output_prefix.gff3";
+ my $bed_file = $gff3_file;
+ $bed_file =~ s/\.gff3$/\.bed/;
+- $cmd = "$UTIL_DIR/gff3_file_to_bed.pl $gff3_file > $bed_file";
++ $cmd = "gff3_file_to_bed.pl $gff3_file > $bed_file";
+ &process_cmd($cmd);
+
+
+ # make a peptide file:
+ my $best_pep_file = $gff3_file;
+ $best_pep_file =~ s/\.gff3$/\.pep/;
+- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
++ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
+ &process_cmd($cmd);
+
+
+@@ -477,13 +476,13 @@
+ # make a CDS file:
+ my $best_cds_file = $best_pep_file;
+ $best_cds_file =~ s/\.pep$/\.cds/;
+- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
++ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
+ &process_cmd($cmd);
+
+ # make a CDS file:
+ my $best_cdna_file = $best_pep_file;
+ $best_cdna_file =~ s/\.pep$/\.mRNA/;
+- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
++ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
+ &process_cmd($cmd);
+
+ }
diff --git a/sci-biology/TransDecoder/files/pfam_runner.pl.patch b/sci-biology/TransDecoder/files/pfam_runner.pl.patch
new file mode 100644
index 0000000..7809b1a
--- /dev/null
+++ b/sci-biology/TransDecoder/files/pfam_runner.pl.patch
@@ -0,0 +1,20 @@
+--- /usr/bin/pfam_runner.pl 2015-01-09 11:22:55.000000000 +0100
++++ pfam_runner.pl 2015-01-09 14:25:43.385838579 +0100
+@@ -24,7 +24,7 @@
+ my $workdir;
+ my $verbose;
+ my ($reuse,$pfam_out);
+-my $CPU = 2;
++my $CPU = 1;
+
+ my $usage = <<_EOH_;
+
+@@ -59,7 +59,7 @@
+ # -h print this option menu and quit
+ # -v verbose
+ #
+-# --CPU <int> number of threads to use; (default: 2)
++# --CPU <int> number of threads to use; (default: 1)
+ #
+ # --MPI use MPI (via ffindex_apply_mpi)
+ #
diff --git a/sci-biology/TransDecoder/metadata.xml b/sci-biology/TransDecoder/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/TransDecoder/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/files/, sci-biology/transdecoder/
@ 2015-04-30 22:51 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-04-30 22:51 UTC (permalink / raw
To: gentoo-commits
commit: e667e2f550d570e61afc091a751729fb166d1913
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 22:50:36 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 22:50:36 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e667e2f5
sci-biology/TransDecoder: renamed package to keep original letter-casing
sci-biology/transdecoder/ChangeLog | 54 --------
sci-biology/transdecoder/files/TransDecoder.patch | 136 ---------------------
.../transdecoder/files/pfam_runner.pl.patch | 20 ---
sci-biology/transdecoder/metadata.xml | 9 --
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 69 -----------
5 files changed, 288 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
deleted file mode 100644
index 6fd8f5c..0000000
--- a/sci-biology/transdecoder/ChangeLog
+++ /dev/null
@@ -1,54 +0,0 @@
-# ChangeLog for sci-biology/transdecoder
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- transdecoder-2.0.1.ebuild:
- sci-biology/transdecoder: more ebuild cleanup
-
- 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- transdecoder-2.0.1.ebuild:
- sci-biology/transdecoder: ebuild cleanup
-
- 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
- sci-biology/transdecoder: drop old
-
- 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
- sci-biology/transdecoder: fixed installation of perl-related files
-
- 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- transdecoder-2.0.1.ebuild:
- dropped hmmer dependency altogether, added pkg_postinst() with
- usage/dependency info
-
-*transdecoder-2.0.1 (19 Mar 2015)
-
- 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
- removing KEYWORDS until the perl files are installed to some other place. At
- the moment I get: 'perl-module.eclass: Suspicious environment values found.
- PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/TransDecoder"'
-
- 15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- transdecoder-20140704.ebuild:
- drop hmmer-3 dependency, it is an optional dependency only
-
- 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- transdecoder-20140704.ebuild:
- install *.pm into PERL5LIB/TransDecoder and pass that via env.d
-
- 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +files/TransDecoder.patch, +files/pfam_runner.pl.patch,
- transdecoder-20140704.ebuild:
- sci-biology/transdecoder: added patches so that we use PATH to loclate
- binaries and not in a local subdirectory named 'util', drop sys-
- cluster/openmpi requirement, it does not link against it all all, this is a
- bunch of perl and shell scripts
-
-*transdecoder-20140704 (08 Jan 2015)
-
- 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
- +transdecoder-20140704.ebuild:
- sci-biology/transdecoder: new package
diff --git a/sci-biology/transdecoder/files/TransDecoder.patch b/sci-biology/transdecoder/files/TransDecoder.patch
deleted file mode 100644
index c0cff94..0000000
--- a/sci-biology/transdecoder/files/TransDecoder.patch
+++ /dev/null
@@ -1,136 +0,0 @@
---- /usr/bin/TransDecoder 2015-01-09 11:22:55.000000000 +0100
-+++ TransDecoder 2015-01-09 14:31:44.095839522 +0100
-@@ -48,7 +48,7 @@
- --prepare_pfam Prepare data for PFAM search and then quit (for running PFAM on HPC/computing cluster
- with or without MPI )
-
-- --CPU <int> number of threads to use; (default: 2)
-+ --CPU <int> number of threads to use; (default: 1)
-
- --MPI use MPI w/ execution of hmmscan
-
-@@ -76,7 +76,7 @@
-
- =head1 PFAM
-
--You will need hmmer installed. Use hmmpress to prepare the database for hmmer.
-+You will need hmmer installed. Use hmmpress from >=hmmer-3.0 to prepare the database for hmmer.
- L<See|https://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin> for downloading the database.
-
- =head1 CD-HIT
-@@ -105,7 +105,6 @@
- use Longest_orf;
-
- my $UTIL_DIR = "$FindBin::RealBin/util";
--$ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
- $ENV{LD_LIBRARY_PATH} .= ":$FindBin::RealBin/util/lib64";
-
- my ($cd_hit_est_exec) = &check_program('cd-hit-est');
-@@ -124,7 +123,7 @@
- my $verbose;
- my $search_pfam = "";
- my ($reuse,$pfam_out);
--my $CPU = 2;
-+my $CPU = 1;
- my $RETAIN_LONG_ORFS = 900;
- my $MPI = 0;
-
-@@ -330,15 +329,15 @@
- my $top_cds_file = $train_file && -s $train_file ? $train_file : "$cds_file.top_${top_ORFs_train}_longest";
- if (!-s $top_cds_file) {
- # get longest entries
-- my $cmd = "$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train > $top_cds_file";
-+ my $cmd = "get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train > $top_cds_file";
-
- unless ($reuse && -s $top_cds_file){
- if ($cd_hit_est_exec){
- # to speed things up only check for redundancy up to 4x the number of entries we want
- my $red_num = $top_ORFs_train * 4 ;
-- &process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file $red_num > $workdir/redundant_top");
-+ &process_cmd("get_top_longest_fasta_entries.pl $cds_file $red_num > $workdir/redundant_top");
- &process_cmd("$cd_hit_est_exec -r 1 -i $workdir/redundant_top -o $workdir/redundant_top.nr90 -M 0 -T $CPU >/dev/null 2>/dev/null");
-- &process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl $workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
-+ &process_cmd("get_top_longest_fasta_entries.pl $workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
- unlink("$workdir/redundant_top");
- unlink("$workdir/redundant_top.nr90");
- unlink("$workdir/redundant_top.nr90.bak.clstr");
-@@ -349,20 +348,20 @@
- }
- }
-
--$cmd = "$UTIL_DIR/compute_base_probs.pl $transcripts_file $TOP_STRAND_ONLY > $workdir/base_freqs.dat";
-+$cmd = "compute_base_probs.pl $transcripts_file $TOP_STRAND_ONLY > $workdir/base_freqs.dat";
- &process_cmd($cmd) unless $reuse && -s "$workdir/base_freqs.dat";
-
-
- # get hexamer scores
--#$cmd = "$UTIL_DIR/seq_n_background_to_logliklihood_vals.pl $top_cds_file $transcripts_file.random > hexamer.scores";
-+#$cmd = "seq_n_background_to_logliklihood_vals.pl $top_cds_file $transcripts_file.random > hexamer.scores";
- #&process_cmd($cmd) unless ($reuse && -s "hexamer.scores");
-
--$cmd = "$UTIL_DIR/seq_n_baseprobs_to_logliklihood_vals.pl $top_cds_file $workdir/base_freqs.dat > $workdir/hexamer.scores";
-+$cmd = "seq_n_baseprobs_to_logliklihood_vals.pl $top_cds_file $workdir/base_freqs.dat > $workdir/hexamer.scores";
- &process_cmd($cmd) unless $reuse && -s "$workdir/hexamer.scores";
-
-
- # score all cds entries
--$cmd = "$UTIL_DIR/score_CDS_liklihood_all_6_frames.pl $cds_file $workdir/hexamer.scores > $cds_file.scores";
-+$cmd = "score_CDS_liklihood_all_6_frames.pl $cds_file $workdir/hexamer.scores > $cds_file.scores";
- &process_cmd($cmd) unless ($reuse && -s "$cds_file.scores");
-
-
-@@ -440,18 +439,18 @@
- }
-
- # index the current gff file:
--$cmd = "$UTIL_DIR/index_gff3_files_by_isoform.pl $gff3_file";
-+$cmd = "index_gff3_files_by_isoform.pl $gff3_file";
- &process_cmd($cmd);
-
- # retrieve the best entries:
--$cmd = "$UTIL_DIR/gene_list_to_gff.pl $acc_file $gff3_file.inx > $cds_file.best_candidates.gff3";
-+$cmd = "gene_list_to_gff.pl $acc_file $gff3_file.inx > $cds_file.best_candidates.gff3";
- &process_cmd($cmd);
-
- {
- my $final_output_prefix = basename($transcripts_file) . ".transdecoder";
-
- # exclude shadow orfs (smaller orfs in different reading frame that are eclipsed by longer orfs)
-- $cmd = "$UTIL_DIR/remove_eclipsed_ORFs.pl $cds_file.best_candidates.gff3 > $final_output_prefix.gff3";
-+ $cmd = "remove_eclipsed_ORFs.pl $cds_file.best_candidates.gff3 > $final_output_prefix.gff3";
- &process_cmd($cmd);
-
-
-@@ -462,14 +461,14 @@
- my $gff3_file = "$final_output_prefix.gff3";
- my $bed_file = $gff3_file;
- $bed_file =~ s/\.gff3$/\.bed/;
-- $cmd = "$UTIL_DIR/gff3_file_to_bed.pl $gff3_file > $bed_file";
-+ $cmd = "gff3_file_to_bed.pl $gff3_file > $bed_file";
- &process_cmd($cmd);
-
-
- # make a peptide file:
- my $best_pep_file = $gff3_file;
- $best_pep_file =~ s/\.gff3$/\.pep/;
-- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
-+ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
- &process_cmd($cmd);
-
-
-@@ -477,13 +476,13 @@
- # make a CDS file:
- my $best_cds_file = $best_pep_file;
- $best_cds_file =~ s/\.pep$/\.cds/;
-- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
-+ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
- &process_cmd($cmd);
-
- # make a CDS file:
- my $best_cdna_file = $best_pep_file;
- $best_cdna_file =~ s/\.pep$/\.mRNA/;
-- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
-+ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
- &process_cmd($cmd);
-
- }
diff --git a/sci-biology/transdecoder/files/pfam_runner.pl.patch b/sci-biology/transdecoder/files/pfam_runner.pl.patch
deleted file mode 100644
index 7809b1a..0000000
--- a/sci-biology/transdecoder/files/pfam_runner.pl.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- /usr/bin/pfam_runner.pl 2015-01-09 11:22:55.000000000 +0100
-+++ pfam_runner.pl 2015-01-09 14:25:43.385838579 +0100
-@@ -24,7 +24,7 @@
- my $workdir;
- my $verbose;
- my ($reuse,$pfam_out);
--my $CPU = 2;
-+my $CPU = 1;
-
- my $usage = <<_EOH_;
-
-@@ -59,7 +59,7 @@
- # -h print this option menu and quit
- # -v verbose
- #
--# --CPU <int> number of threads to use; (default: 2)
-+# --CPU <int> number of threads to use; (default: 1)
- #
- # --MPI use MPI (via ffindex_apply_mpi)
- #
diff --git a/sci-biology/transdecoder/metadata.xml b/sci-biology/transdecoder/metadata.xml
deleted file mode 100644
index 2bc8930..0000000
--- a/sci-biology/transdecoder/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
deleted file mode 100644
index e8f5134..0000000
--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
-HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
-SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/cd-hit
- sci-biology/hmmer
- sci-biology/parafly
- sci-biology/ffindex"
-# cdhit-4.6.1 is a real dependency, at least hmmer is optional (also ncbi-tools++ is now used for ORF searches)
-
-S="${WORKDIR}"/TransDecoder-2.0.1
-
-##src_prepare(){
-# #mv Makefile Makefile.old
-# #epatch "${FILESDIR}"/TransDecoder.patch
-# #epatch "${FILESDIR}"/pfam_runner.pl.patch
-#}
-
-# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
-# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
-#
-# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
-
-src_install(){
- dobin TransDecoder.Predict TransDecoder.LongOrfs
- insinto /usr/share/${PN}/util
- dobin util/*.pl
- # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
- rm -rf util/bin
- #
- # * sci-biology/trinityrnaseq-20140413:0::science
- # * /usr/bin/Fasta_reader.pm
- # * /usr/bin/GFF3_utils.pm
- # * /usr/bin/Gene_obj.pm
- # * /usr/bin/Gene_obj_indexer.pm
- # * /usr/bin/Longest_orf.pm
- # * /usr/bin/Nuc_translator.pm
- # * /usr/bin/TiedHash.pm
- #
- perl_set_version
- insinto ${VENDOR_LIB}/${PN}
- dobin PerlLib/*.pm # BUG: install into /usr/bin but wanted to have it readable and executable in ${VENDOR_LIB}/${PN} instead
- einfo "Fetch on your own:"
- einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
- einfo "hmmpress Pfam-AB.hmm.bin"
-}
-
-pkg_postinst(){
- einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast"
- einfo "from either sci-biology/ncbi-blast+ (released more often) or"
- einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)"
- einfo "Author says the minimum requirement is sci-biology/cd-hit"
-}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/
@ 2015-11-19 20:29 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-11-19 20:29 UTC (permalink / raw
To: gentoo-commits
commit: 8f7a916bbdbb62d44a963c77692e3895d6b838ba
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 20:28:40 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 20:28:40 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f7a916b
sci-biology/TransDecoder: install properly perl modules; fix PERL5INC paths by adding TransDecoder::, ebuild cleanup
Package-Manager: portage-2.2.18
sci-biology/TransDecoder/ChangeLog | 6 +
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 52 +++++---
.../files/TransDecoder-2.0.1__fix_paths.patch | 22 ++++
sci-biology/TransDecoder/files/TransDecoder.patch | 136 ---------------------
.../TransDecoder/files/pfam_runner.pl.patch | 4 +-
5 files changed, 63 insertions(+), 157 deletions(-)
diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog
index 680a908..67b410e 100644
--- a/sci-biology/TransDecoder/ChangeLog
+++ b/sci-biology/TransDecoder/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/TransDecoder-2.0.1__fix_paths.patch, -files/TransDecoder.patch,
+ TransDecoder-2.0.1.ebuild, files/pfam_runner.pl.patch:
+ sci-biology/TransDecoder: install properly perl modules; fix PERL5INC paths by
+ adding TransDecoder::, ebuild cleanup
+
06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
sci-biology/TransDecoder: Add github to remote-id in metadata.xml
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
index b99375f..5894f2a 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -4,43 +4,56 @@
EAPI=5
+[ "$PV" == "9999" ] && inherit git-r3
+
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
-SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
+ KEYWORDS=""
+else
+ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64"
+ S="${WORKDIR}"/TransDecoder-"${PV}"
+fi
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS="~amd64"
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/cd-hit
- sci-biology/hmmer
sci-biology/parafly
sci-biology/ffindex"
-# cdhit-4.6.1 is a real dependency, at least hmmer is optional (also ncbi-tools++ is now used for ORF searches)
-S="${WORKDIR}"/TransDecoder-2.0.1
+src_prepare(){
+ rm -rf transdecoder_plugins/cd-hit
+ for f in PerlLib/*.pm; do
+ p=`basename $f .pm`;
+ sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict;
+ done
+ epatch "${FILESDIR}"/"${P}"__fix_paths.patch
+ epatch "${FILESDIR}"/pfam_runner.pl.patch
+}
-##src_prepare(){
-# #mv Makefile Makefile.old
-# #epatch "${FILESDIR}"/TransDecoder.patch
-# #epatch "${FILESDIR}"/pfam_runner.pl.patch
-#}
+src_compile(){
+ einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
+}
# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
-# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
-#
-# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
+# thread in archives. You can get it from
+# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
src_install(){
dobin TransDecoder.Predict TransDecoder.LongOrfs
insinto /usr/share/${PN}/util
- dobin util/*.pl
+ doins util/*.pl
+ chmod -R a+rx "${D}"/usr/share/${PN}/util
# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
rm -rf util/bin
#
@@ -55,15 +68,16 @@ src_install(){
#
perl_set_version
insinto ${VENDOR_LIB}/${PN}
- dobin PerlLib/*.pm # BUG: install into /usr/bin but wanted to have it readable and executable in ${VENDOR_LIB}/${PN} instead
+ doins PerlLib/*.pm
+ dodoc Release.Notes
einfo "Fetch on your own:"
einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
einfo "hmmpress Pfam-AB.hmm.bin"
}
pkg_postinst(){
- einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast"
- einfo "from either sci-biology/ncbi-blast+ (released more often) or"
- einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)"
- einfo "Author says the minimum requirement is sci-biology/cd-hit"
+ einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
+ einfo "at least with NCBI blast from either:"
+ einfo " sci-biology/ncbi-blast+ (released more often) or from"
+ einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
}
diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch
new file mode 100644
index 0000000..0a6fca0
--- /dev/null
+++ b/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch
@@ -0,0 +1,22 @@
+--- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100
++++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100
+@@ -64,7 +64,7 @@
+ use TransDecoder::Fasta_reader;
+ use TransDecoder::Longest_orf;
+
+-my $UTIL_DIR = "$FindBin::RealBin/util";
++my $UTIL_DIR = "/usr/share/TransDecoder/util/";
+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+
+
+--- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100
++++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100
+@@ -52,7 +52,7 @@
+ use TransDecoder::Fasta_reader;
+ use TransDecoder::Longest_orf;
+
+-my $UTIL_DIR = "$FindBin::RealBin/util";
++my $UTIL_DIR = "/usr/share/TransDecoder/util/";
+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+
+
diff --git a/sci-biology/TransDecoder/files/TransDecoder.patch b/sci-biology/TransDecoder/files/TransDecoder.patch
deleted file mode 100644
index c0cff94..0000000
--- a/sci-biology/TransDecoder/files/TransDecoder.patch
+++ /dev/null
@@ -1,136 +0,0 @@
---- /usr/bin/TransDecoder 2015-01-09 11:22:55.000000000 +0100
-+++ TransDecoder 2015-01-09 14:31:44.095839522 +0100
-@@ -48,7 +48,7 @@
- --prepare_pfam Prepare data for PFAM search and then quit (for running PFAM on HPC/computing cluster
- with or without MPI )
-
-- --CPU <int> number of threads to use; (default: 2)
-+ --CPU <int> number of threads to use; (default: 1)
-
- --MPI use MPI w/ execution of hmmscan
-
-@@ -76,7 +76,7 @@
-
- =head1 PFAM
-
--You will need hmmer installed. Use hmmpress to prepare the database for hmmer.
-+You will need hmmer installed. Use hmmpress from >=hmmer-3.0 to prepare the database for hmmer.
- L<See|https://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin> for downloading the database.
-
- =head1 CD-HIT
-@@ -105,7 +105,6 @@
- use Longest_orf;
-
- my $UTIL_DIR = "$FindBin::RealBin/util";
--$ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
- $ENV{LD_LIBRARY_PATH} .= ":$FindBin::RealBin/util/lib64";
-
- my ($cd_hit_est_exec) = &check_program('cd-hit-est');
-@@ -124,7 +123,7 @@
- my $verbose;
- my $search_pfam = "";
- my ($reuse,$pfam_out);
--my $CPU = 2;
-+my $CPU = 1;
- my $RETAIN_LONG_ORFS = 900;
- my $MPI = 0;
-
-@@ -330,15 +329,15 @@
- my $top_cds_file = $train_file && -s $train_file ? $train_file : "$cds_file.top_${top_ORFs_train}_longest";
- if (!-s $top_cds_file) {
- # get longest entries
-- my $cmd = "$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train > $top_cds_file";
-+ my $cmd = "get_top_longest_fasta_entries.pl $cds_file $top_ORFs_train > $top_cds_file";
-
- unless ($reuse && -s $top_cds_file){
- if ($cd_hit_est_exec){
- # to speed things up only check for redundancy up to 4x the number of entries we want
- my $red_num = $top_ORFs_train * 4 ;
-- &process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl $cds_file $red_num > $workdir/redundant_top");
-+ &process_cmd("get_top_longest_fasta_entries.pl $cds_file $red_num > $workdir/redundant_top");
- &process_cmd("$cd_hit_est_exec -r 1 -i $workdir/redundant_top -o $workdir/redundant_top.nr90 -M 0 -T $CPU >/dev/null 2>/dev/null");
-- &process_cmd("$UTIL_DIR/get_top_longest_fasta_entries.pl $workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
-+ &process_cmd("get_top_longest_fasta_entries.pl $workdir/redundant_top.nr90 $top_ORFs_train > $top_cds_file");
- unlink("$workdir/redundant_top");
- unlink("$workdir/redundant_top.nr90");
- unlink("$workdir/redundant_top.nr90.bak.clstr");
-@@ -349,20 +348,20 @@
- }
- }
-
--$cmd = "$UTIL_DIR/compute_base_probs.pl $transcripts_file $TOP_STRAND_ONLY > $workdir/base_freqs.dat";
-+$cmd = "compute_base_probs.pl $transcripts_file $TOP_STRAND_ONLY > $workdir/base_freqs.dat";
- &process_cmd($cmd) unless $reuse && -s "$workdir/base_freqs.dat";
-
-
- # get hexamer scores
--#$cmd = "$UTIL_DIR/seq_n_background_to_logliklihood_vals.pl $top_cds_file $transcripts_file.random > hexamer.scores";
-+#$cmd = "seq_n_background_to_logliklihood_vals.pl $top_cds_file $transcripts_file.random > hexamer.scores";
- #&process_cmd($cmd) unless ($reuse && -s "hexamer.scores");
-
--$cmd = "$UTIL_DIR/seq_n_baseprobs_to_logliklihood_vals.pl $top_cds_file $workdir/base_freqs.dat > $workdir/hexamer.scores";
-+$cmd = "seq_n_baseprobs_to_logliklihood_vals.pl $top_cds_file $workdir/base_freqs.dat > $workdir/hexamer.scores";
- &process_cmd($cmd) unless $reuse && -s "$workdir/hexamer.scores";
-
-
- # score all cds entries
--$cmd = "$UTIL_DIR/score_CDS_liklihood_all_6_frames.pl $cds_file $workdir/hexamer.scores > $cds_file.scores";
-+$cmd = "score_CDS_liklihood_all_6_frames.pl $cds_file $workdir/hexamer.scores > $cds_file.scores";
- &process_cmd($cmd) unless ($reuse && -s "$cds_file.scores");
-
-
-@@ -440,18 +439,18 @@
- }
-
- # index the current gff file:
--$cmd = "$UTIL_DIR/index_gff3_files_by_isoform.pl $gff3_file";
-+$cmd = "index_gff3_files_by_isoform.pl $gff3_file";
- &process_cmd($cmd);
-
- # retrieve the best entries:
--$cmd = "$UTIL_DIR/gene_list_to_gff.pl $acc_file $gff3_file.inx > $cds_file.best_candidates.gff3";
-+$cmd = "gene_list_to_gff.pl $acc_file $gff3_file.inx > $cds_file.best_candidates.gff3";
- &process_cmd($cmd);
-
- {
- my $final_output_prefix = basename($transcripts_file) . ".transdecoder";
-
- # exclude shadow orfs (smaller orfs in different reading frame that are eclipsed by longer orfs)
-- $cmd = "$UTIL_DIR/remove_eclipsed_ORFs.pl $cds_file.best_candidates.gff3 > $final_output_prefix.gff3";
-+ $cmd = "remove_eclipsed_ORFs.pl $cds_file.best_candidates.gff3 > $final_output_prefix.gff3";
- &process_cmd($cmd);
-
-
-@@ -462,14 +461,14 @@
- my $gff3_file = "$final_output_prefix.gff3";
- my $bed_file = $gff3_file;
- $bed_file =~ s/\.gff3$/\.bed/;
-- $cmd = "$UTIL_DIR/gff3_file_to_bed.pl $gff3_file > $bed_file";
-+ $cmd = "gff3_file_to_bed.pl $gff3_file > $bed_file";
- &process_cmd($cmd);
-
-
- # make a peptide file:
- my $best_pep_file = $gff3_file;
- $best_pep_file =~ s/\.gff3$/\.pep/;
-- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
-+ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
- &process_cmd($cmd);
-
-
-@@ -477,13 +476,13 @@
- # make a CDS file:
- my $best_cds_file = $best_pep_file;
- $best_cds_file =~ s/\.pep$/\.cds/;
-- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
-+ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
- &process_cmd($cmd);
-
- # make a CDS file:
- my $best_cdna_file = $best_pep_file;
- $best_cdna_file =~ s/\.pep$/\.mRNA/;
-- $cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
-+ $cmd = "gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
- &process_cmd($cmd);
-
- }
diff --git a/sci-biology/TransDecoder/files/pfam_runner.pl.patch b/sci-biology/TransDecoder/files/pfam_runner.pl.patch
index 7809b1a..fbc6f6d 100644
--- a/sci-biology/TransDecoder/files/pfam_runner.pl.patch
+++ b/sci-biology/TransDecoder/files/pfam_runner.pl.patch
@@ -1,5 +1,5 @@
---- /usr/bin/pfam_runner.pl 2015-01-09 11:22:55.000000000 +0100
-+++ pfam_runner.pl 2015-01-09 14:25:43.385838579 +0100
+--- util/pfam_runner.pl 2015-01-09 11:22:55.000000000 +0100
++++ util/pfam_runner.pl 2015-01-09 14:25:43.385838579 +0100
@@ -24,7 +24,7 @@
my $workdir;
my $verbose;
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/
@ 2017-09-07 20:49 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2017-09-07 20:49 UTC (permalink / raw
To: gentoo-commits
commit: 539fae1fd1daad0dc762aaa66fcb6fcec4d46bdc
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 7 20:49:10 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep 7 20:49:10 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=539fae1f
sci-biology/TransDecoder: Remove old
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 82 ----------------------
.../files/TransDecoder-2.0.1__fix_paths.patch | 22 ------
2 files changed, 104 deletions(-)
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
deleted file mode 100644
index 1e5f1ad23..000000000
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-[ "$PV" == "9999" ] && inherit git-r3
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
-HOMEPAGE="http://transdecoder.github.io"
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
- KEYWORDS=""
-else
- SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64"
- S="${WORKDIR}"/TransDecoder-"${PV}"
-fi
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/cd-hit
- sci-biology/parafly
- sci-biology/ffindex"
-
-src_prepare(){
- rm -rf transdecoder_plugins/cd-hit
- for f in PerlLib/*.pm; do
- p=`basename $f .pm`;
- sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die;
- done
- epatch "${FILESDIR}"/"${P}"__fix_paths.patch
- epatch "${FILESDIR}"/pfam_runner.pl.patch
-}
-
-src_compile(){
- einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
-}
-
-# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
-# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
-# thread in archives. You can get it from
-# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
-
-src_install(){
- dobin TransDecoder.Predict TransDecoder.LongOrfs
- insinto /usr/share/${PN}/util
- doins util/*.pl
- chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util || die
- # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
- rm -rf util/bin
- #
- # * sci-biology/trinityrnaseq-20140413:0::science
- # * /usr/bin/Fasta_reader.pm
- # * /usr/bin/GFF3_utils.pm
- # * /usr/bin/Gene_obj.pm
- # * /usr/bin/Gene_obj_indexer.pm
- # * /usr/bin/Longest_orf.pm
- # * /usr/bin/Nuc_translator.pm
- # * /usr/bin/TiedHash.pm
- #
- perl_set_version
- insinto ${VENDOR_LIB}/${PN}
- doins PerlLib/*.pm
- dodoc Release.Notes
- einfo "Fetch on your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
- einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
- einfo "hmmpress Pfam-A.hmm.bin"
-}
-
-pkg_postinst(){
- einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
- einfo "at least with NCBI blast from either:"
- einfo " sci-biology/ncbi-blast+ (released more often) or from"
- einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
-}
diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch
deleted file mode 100644
index 0a6fca050..000000000
--- a/sci-biology/TransDecoder/files/TransDecoder-2.0.1__fix_paths.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100
-+++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100
-@@ -64,7 +64,7 @@
- use TransDecoder::Fasta_reader;
- use TransDecoder::Longest_orf;
-
--my $UTIL_DIR = "$FindBin::RealBin/util";
-+my $UTIL_DIR = "/usr/share/TransDecoder/util/";
- $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
-
-
---- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100
-+++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100
-@@ -52,7 +52,7 @@
- use TransDecoder::Fasta_reader;
- use TransDecoder::Longest_orf;
-
--my $UTIL_DIR = "$FindBin::RealBin/util";
-+my $UTIL_DIR = "/usr/share/TransDecoder/util/";
- $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
-
-
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/
@ 2017-09-07 20:49 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2017-09-07 20:49 UTC (permalink / raw
To: gentoo-commits
commit: 6f631fd58c22a7c42ece339ec8d5ead6d53f55fe
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 7 20:47:27 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep 7 20:47:34 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f631fd5
sci-biology/TransDecoder: Fix double-prefix
Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild | 68 +++++++++-------------
.../TransDecoder/files/pfam_runner.pl.patch | 4 +-
2 files changed, 31 insertions(+), 41 deletions(-)
diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
index bb592938e..6b462ff90 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
@@ -1,45 +1,47 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-[ "$PV" == "9999" ] && inherit git-r3
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-functions toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="http://transdecoder.github.io"
-if [ "$PV" == "9999" ]; then
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
- KEYWORDS=""
else
- SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz"
+ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v${PV}.tar.gz -> ${P}.tar.gz"
KEYWORDS="~amd64"
- S="${WORKDIR}"/TransDecoder-"${PV}"
fi
LICENSE="BSD-BroadInstitute"
SLOT="0"
IUSE=""
-DEPEND=""
+DEPEND="dev-lang/perl:="
RDEPEND="${DEPEND}
sci-biology/cd-hit
sci-biology/parafly
sci-biology/ffindex"
-src_prepare(){
- rm -rf transdecoder_plugins/cd-hit
+src_prepare() {
+ rm -rf transdecoder_plugins/cd-hit || die
+ local f p
for f in PerlLib/*.pm; do
- p=`basename $f .pm`;
- sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die;
+ p=$(basename $f .pm)
+
+ sed -e "s#use $p;#use TransDecoder::$p;#" \
+ -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die
done
- epatch "${FILESDIR}"/"${P}"__fix_paths.patch
- epatch "${FILESDIR}"/pfam_runner.pl.patch
+ eapply "${FILESDIR}"/"${P}"__fix_paths.patch
+ eapply "${FILESDIR}"/pfam_runner.pl.patch
+
+ eapply_user
}
-src_compile(){
+src_compile() {
einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
}
@@ -48,37 +50,25 @@ src_compile(){
# thread in archives. You can get it from
# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
-src_install(){
+src_install() {
dobin TransDecoder.Predict TransDecoder.LongOrfs
+
insinto /usr/share/${PN}/util
doins util/*.pl
- chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util || die
+
+ chmod -R a+rx "${ED%/}"/usr/share/${PN}/util || die
# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
- rm -rf util/bin
- #
- # * sci-biology/trinityrnaseq-20140413:0::science
- # * /usr/bin/Fasta_reader.pm
- # * /usr/bin/GFF3_utils.pm
- # * /usr/bin/Gene_obj.pm
- # * /usr/bin/Gene_obj_indexer.pm
- # * /usr/bin/Longest_orf.pm
- # * /usr/bin/Nuc_translator.pm
- # * /usr/bin/TiedHash.pm
- #
- perl_set_version
- # this is broken and installs into
- # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/
- # instead of
- # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/
- insinto ${VENDOR_LIB}/${PN}
- doins PerlLib/*.pm
+ rm -rf util/bin || die
+
+ perl_domodule -C ${PN} PerlLib/*.pm
+
# dodoc Release.Notes
einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
einfo "hmmpress Pfam-A.hmm.bin"
}
-pkg_postinst(){
+pkg_postinst() {
einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
einfo "at least with NCBI blast from either:"
einfo " sci-biology/ncbi-blast+ (released more often) or from"
diff --git a/sci-biology/TransDecoder/files/pfam_runner.pl.patch b/sci-biology/TransDecoder/files/pfam_runner.pl.patch
index fbc6f6d92..1e8b96cc7 100644
--- a/sci-biology/TransDecoder/files/pfam_runner.pl.patch
+++ b/sci-biology/TransDecoder/files/pfam_runner.pl.patch
@@ -1,5 +1,5 @@
---- util/pfam_runner.pl 2015-01-09 11:22:55.000000000 +0100
-+++ util/pfam_runner.pl 2015-01-09 14:25:43.385838579 +0100
+--- a/util/pfam_runner.pl
++++ b/util/pfam_runner.pl
@@ -24,7 +24,7 @@
my $workdir;
my $verbose;
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/
@ 2021-01-18 13:31 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 13:31 UTC (permalink / raw
To: gentoo-commits
commit: 205a84fd4e41b0c09494d8edad2bff30f9610ba3
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 13:30:41 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 13:30:41 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=205a84fd
sci-biology/TransDecoder: version bump 5.5.0, fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
...oder-2.1.0.ebuild => TransDecoder-5.5.0.ebuild} | 13 +++++++------
.../files/TransDecoder-2.1.0__fix_paths.patch | 22 ----------------------
2 files changed, 7 insertions(+), 28 deletions(-)
diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
similarity index 88%
rename from sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
rename to sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
index 6b462ff90..c485d4b86 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
@@ -1,24 +1,26 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit perl-functions toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
-HOMEPAGE="http://transdecoder.github.io"
+HOMEPAGE="https://github.com/TransDecoder/TransDecoder/wiki"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
else
- SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v${PV}.tar.gz"
KEYWORDS="~amd64"
+ S="${WORKDIR}/${PN}-${PN}-v${PV}"
fi
LICENSE="BSD-BroadInstitute"
SLOT="0"
-IUSE=""
+
+RESTRICT="test"
DEPEND="dev-lang/perl:="
RDEPEND="${DEPEND}
@@ -35,7 +37,6 @@ src_prepare() {
sed -e "s#use $p;#use TransDecoder::$p;#" \
-i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die
done
- eapply "${FILESDIR}"/"${P}"__fix_paths.patch
eapply "${FILESDIR}"/pfam_runner.pl.patch
eapply_user
diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
deleted file mode 100644
index 0a6fca050..000000000
--- a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100
-+++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100
-@@ -64,7 +64,7 @@
- use TransDecoder::Fasta_reader;
- use TransDecoder::Longest_orf;
-
--my $UTIL_DIR = "$FindBin::RealBin/util";
-+my $UTIL_DIR = "/usr/share/TransDecoder/util/";
- $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
-
-
---- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100
-+++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100
-@@ -52,7 +52,7 @@
- use TransDecoder::Fasta_reader;
- use TransDecoder::Longest_orf;
-
--my $UTIL_DIR = "$FindBin::RealBin/util";
-+my $UTIL_DIR = "/usr/share/TransDecoder/util/";
- $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
-
-
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2021-01-18 13:31 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2017-09-07 20:49 [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/ David Seifert
-- strict thread matches above, loose matches on Subject: below --
2021-01-18 13:31 Andrew Ammerlaan
2017-09-07 20:49 David Seifert
2015-11-19 20:29 Martin Mokrejs
2015-04-30 22:51 [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/files/, sci-biology/transdecoder/ Martin Mokrejs
2015-04-30 22:48 [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/files/, sci-biology/TransDecoder/ Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox