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 <mmokr...@fold.natur.cuni.cz> - transdecoder-2.0.1.ebuild: - sci-biology/transdecoder: more ebuild cleanup - - 27 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> - transdecoder-2.0.1.ebuild: - sci-biology/transdecoder: ebuild cleanup - - 27 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> - -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild: - sci-biology/transdecoder: drop old - - 17 Apr 2015; Martin Mokrejs <mmokr...@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 <mmokr...@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 <mmokr...@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 <mmokr...@fold.natur.cuni.cz> - transdecoder-20140704.ebuild: - drop hmmer-3 dependency, it is an optional dependency only - - 10 Jan 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> - transdecoder-20140704.ebuild: - install *.pm into PERL5LIB/TransDecoder and pass that via env.d - - 09 Jan 2015; Martin Mokrejs <mmokr...@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 <mmokr...@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>mmokr...@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" -}
