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Import p5-transdecoder-2.0.1 as wip/p5-transdecoder.
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Wed May 11 07:29:48 2016 -0500
Changeset: 7073f87e37e13b515bdcfc1d323861c0c433106b
Added Files:
p5-transdecoder/DESCR
p5-transdecoder/Makefile
p5-transdecoder/PLIST
p5-transdecoder/TODO
p5-transdecoder/distinfo
Log Message:
Import p5-transdecoder-2.0.1 as wip/p5-transdecoder.
TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7073f87e37e13b515bdcfc1d323861c0c433106b
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
p5-transdecoder/DESCR | 4 ++++
p5-transdecoder/Makefile | 52 ++++++++++++++++++++++++++++++++++++++++++++++++
p5-transdecoder/PLIST | 26 ++++++++++++++++++++++++
p5-transdecoder/TODO | 1 +
p5-transdecoder/distinfo | 5 +++++
5 files changed, 88 insertions(+)
diffs:
diff --git a/p5-transdecoder/DESCR b/p5-transdecoder/DESCR
new file mode 100644
index 0000000..a24d00f
--- /dev/null
+++ b/p5-transdecoder/DESCR
@@ -0,0 +1,4 @@
+TransDecoder identifies candidate coding regions within transcript sequences,
+such as those generated by de novo RNA-Seq transcript assembly using Trinity,
+or constructed based on RNA-Seq alignments to the genome using Tophat and
+Cufflinks.
diff --git a/p5-transdecoder/Makefile b/p5-transdecoder/Makefile
new file mode 100644
index 0000000..3b9955e
--- /dev/null
+++ b/p5-transdecoder/Makefile
@@ -0,0 +1,52 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+###########################################################
+
+# TransDecoder.LongOrfs suggests doing Pfam or BlastP searches?
+# p5-URI-ESC?
+# FIXME: Check use statements in all perl scripts for more deps
+
+DISTNAME= p5-transdecoder-${PORTVERSION}
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=TransDecoder/}
+GITHUB_PROJECT= TransDecoder
+GITHUB_TAG= ${PORTVERSION}
+
+MAINTAINER= bacon4000%gmail.com@localhost
+HOMEPAGE= http://transdecoder.github.io/
+COMMENT= Identify candidate coding regions within transcript sequences
+LICENSE= modified-bsd
+
+SUBST_CLASSES+= path
+SUBST_STAGE.path= post-patch
+SUBST_SED.path+= -e 's|$$FindBin::RealBin/PerlLib|${PREFIX}/lib/TransDecoder/PerlLib|g'
+SUBST_SED.path+= -e 's|$$FindBin::Bin/../PerlLib|${PREFIX}/lib/TransDecoder/PerlLib|g'
+SUBST_SED.path+= -e 's|$$FindBin::RealBin/util|${PREFIX}/libexec/TransDecoder/util|g'
+SUBST_FILES.path+= ${WRKSRC}/TransDecoder*
+SUBST_FILES.path+= ${WRKSRC}/util/*.pl
+
+DEPENDS= cdhit>=4.6.1:../../biology/cdhit \
+ p5-URI>=0:../../www/p5-URI
+
+USE_TOOLS= perl
+REPLACE_BASH= sample_data/runMe.sh util/pfam_mpi.pbs
+REPLACE_PERL= util/*.pl sample_data/*.pl PerlLib/*.pm \
+ TransDecoder.LongOrfs TransDecoder.Predict
+NO_BUILD= yes
+
+FETCH_USING= curl
+
+PORTVERSION= 2.0.1
+
+INSTALLATION_DIRS= bin lib/TransDecoder/PerlLib libexec/TransDecoder/util
+
+do-install:
+ ${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* \
+ ${DESTDIR}${PREFIX}/lib/TransDecoder/PerlLib
+ ${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${DESTDIR}${PREFIX}/bin
+ ${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl \
+ ${DESTDIR}${PREFIX}/libexec/TransDecoder/util
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/p5-transdecoder/PLIST b/p5-transdecoder/PLIST
new file mode 100644
index 0000000..a652fb4
--- /dev/null
+++ b/p5-transdecoder/PLIST
@@ -0,0 +1,26 @@
+@comment $NetBSD$
+bin/TransDecoder.LongOrfs
+bin/TransDecoder.Predict
+libexec/TransDecoder/util/cdna_alignment_orf_to_genome_orf.pl
+libexec/TransDecoder/util/compute_base_probs.pl
+libexec/TransDecoder/util/cufflinks_gtf_genome_to_cdna_fasta.pl
+libexec/TransDecoder/util/cufflinks_gtf_to_alignment_gff3.pl
+libexec/TransDecoder/util/cufflinks_gtf_to_bed.pl
+libexec/TransDecoder/util/ffindex_resume.pl
+libexec/TransDecoder/util/gene_list_to_gff.pl
+libexec/TransDecoder/util/get_top_longest_fasta_entries.pl
+libexec/TransDecoder/util/gff3_file_to_bed.pl
+libexec/TransDecoder/util/gff3_file_to_proteins.pl
+libexec/TransDecoder/util/index_gff3_files_by_isoform.pl
+libexec/TransDecoder/util/nr_ORFs_gff3.pl
+libexec/TransDecoder/util/pfam_runner.pl
+libexec/TransDecoder/util/remove_eclipsed_ORFs.pl
+libexec/TransDecoder/util/score_CDS_liklihood_all_6_frames.pl
+libexec/TransDecoder/util/seq_n_baseprobs_to_logliklihood_vals.pl
+lib/TransDecoder/PerlLib/Fasta_reader.pm
+lib/TransDecoder/PerlLib/Gene_obj_indexer.pm
+lib/TransDecoder/PerlLib/Gene_obj.pm
+lib/TransDecoder/PerlLib/GFF3_utils.pm
+lib/TransDecoder/PerlLib/Longest_orf.pm
+lib/TransDecoder/PerlLib/Nuc_translator.pm
+lib/TransDecoder/PerlLib/TiedHash.pm
diff --git a/p5-transdecoder/TODO b/p5-transdecoder/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/p5-transdecoder/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/p5-transdecoder/distinfo b/p5-transdecoder/distinfo
new file mode 100644
index 0000000..a6ba935
--- /dev/null
+++ b/p5-transdecoder/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+SHA1 (p5-transdecoder-2.0.1.tar.gz) = 1a36aa7ecb3af9e984eb9bee818871093fa1ab74
+RMD160 (p5-transdecoder-2.0.1.tar.gz) = d59644fc9f44f428ae5f001543e33ca3b7539aec
+Size (p5-transdecoder-2.0.1.tar.gz) = 9925281 bytes
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