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 <mmokr...@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 <j...@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;
