Import p5-transdecoder-2.0.1 as wip/p5-transdecoder.

[Jason Bacon <bacon4000%gmail.com@localhost>]

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