[gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/files/, sci-biology/transdecoder/

[Martin Mokrejs]

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@×××××××××××××××.cz>
-  transdecoder-2.0.1.ebuild:
-  sci-biology/transdecoder: more ebuild cleanup
-
-  27 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
-  transdecoder-2.0.1.ebuild:
-  sci-biology/transdecoder: ebuild cleanup
-
-  27 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
-  -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
-  sci-biology/transdecoder: drop old
-
-  17 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
-  transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
-  sci-biology/transdecoder: fixed installation of perl-related files
-
-  19 Mar 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.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@×××××××××××××××.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@×××××××××××××××.cz>
-  transdecoder-20140704.ebuild:
-  drop hmmer-3 dependency, it is an optional dependency only
-
-  10 Jan 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
-  transdecoder-20140704.ebuild:
-  install *.pm into PERL5LIB/TransDecoder and pass that via env.d
-
-  09 Jan 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.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@×××××××××××××××.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@×××××××××××××××.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"
-}