New port: biology/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.

WWW: http://transdecoder.github.io/

PR:		207993
Submitted by:	Jason Bacon <bacon4000@gmail.com>

5 files changed, 88 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 25eb27f25ddd..08458a335d1c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -65,6 +65,7 @@
     SUBDIR += p5-Bio-SCF
     SUBDIR += p5-bioperl
     SUBDIR += p5-bioperl-run
+    SUBDIR += p5-transdecoder
     SUBDIR += paml
     SUBDIR += phrap
     SUBDIR += phred
diff --git a/biology/p5-transdecoder/Makefile b/biology/p5-transdecoder/Makefile
new file mode 100644
index 000000000000..fc0f578bf8a1
--- /dev/null
+++ b/biology/p5-transdecoder/Makefile
@@ -0,0 +1,47 @@
+# Created by: Jason Bacon <bacon4000@gmail.com>
+# $FreeBSD$
+
+PORTNAME=	transdecoder
+PORTVERSION=	2.1.0
+DISTVERSIONPREFIX=v
+CATEGORIES=	biology perl5
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	bacon4000@gmail.com
+COMMENT=	Identify candidate coding regions within transcript sequences
+
+LICENSE=	BSD3CLAUSE
+
+RUN_DEPENDS=	cd-hit>=4.6.1:${PORTSDIR}/biology/cd-hit \
+		p5-URI>0:${PORTSDIR}/net/p5-URI
+
+NO_BUILD=	yes
+NO_ARCH=	yes
+USES=		perl5 shebangfix
+SHEBANG_FILES=	sample_data/cufflinks_example/runMe.sh \
+		sample_data/pasa_example/runMe.sh \
+		sample_data/simple_transcriptome_target/runMe.sh \
+		util/pfam_mpi.pbs
+
+USE_GITHUB=	yes
+GH_PROJECT=	TransDecoder
+
+WRKSRC=		${WRKDIR}/${GH_PROJECT}-${PORTVERSION}
+
+PERL_MOD_DIR=	${PREFIX}/${SITE_PERL_REL}/${PORTNAME}
+PERL_UTIL_DIR=	${PREFIX}/libexec/${PORTNAME}
+
+post-patch:
+	${REINPLACE_CMD} \
+		-e 's|$$FindBin::RealBin/PerlLib|${PERL_MOD_DIR}|g' \
+		-e 's|$$FindBin::Bin/../PerlLib|${PERL_MOD_DIR}|g' \
+		-e 's|$$FindBin::RealBin/util|${PERL_UTIL_DIR}|g' \
+		${WRKSRC}/TransDecoder* ${WRKSRC}/util/*.pl
+
+do-install:
+	${MKDIR} ${STAGEDIR}${PERL_MOD_DIR} ${STAGEDIR}${PERL_UTIL_DIR}
+	${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* ${STAGEDIR}${PERL_MOD_DIR}
+	${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl ${STAGEDIR}${PERL_UTIL_DIR}
+
+.include <bsd.port.mk>
diff --git a/biology/p5-transdecoder/distinfo b/biology/p5-transdecoder/distinfo
new file mode 100644
index 000000000000..bf42546af4c0
--- /dev/null
+++ b/biology/p5-transdecoder/distinfo
@@ -0,0 +1,2 @@
+SHA256 (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24
+SIZE (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 11500688
diff --git a/biology/p5-transdecoder/pkg-descr b/biology/p5-transdecoder/pkg-descr
new file mode 100644
index 000000000000..7cb7ca555079
--- /dev/null
+++ b/biology/p5-transdecoder/pkg-descr
@@ -0,0 +1,6 @@
+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.
+
+WWW: http://transdecoder.github.io/
diff --git a/biology/p5-transdecoder/pkg-plist b/biology/p5-transdecoder/pkg-plist
new file mode 100644
index 000000000000..d394d7fa2914
--- /dev/null
+++ b/biology/p5-transdecoder/pkg-plist
@@ -0,0 +1,32 @@
+bin/TransDecoder.LongOrfs
+bin/TransDecoder.LongOrfs.bak
+bin/TransDecoder.Predict
+bin/TransDecoder.Predict.bak
+%%SITE_PERL%%/transdecoder/Fasta_reader.pm
+%%SITE_PERL%%/transdecoder/Fasta_retriever.pm
+%%SITE_PERL%%/transdecoder/GFF3_utils.pm
+%%SITE_PERL%%/transdecoder/Gene_obj.pm
+%%SITE_PERL%%/transdecoder/Gene_obj_indexer.pm
+%%SITE_PERL%%/transdecoder/Longest_orf.pm
+%%SITE_PERL%%/transdecoder/Nuc_translator.pm
+%%SITE_PERL%%/transdecoder/TiedHash.pm
+libexec/transdecoder/cdna_alignment_orf_to_genome_orf.pl
+libexec/transdecoder/compute_base_probs.pl
+libexec/transdecoder/create_start_PSSM.pl
+libexec/transdecoder/cufflinks_gtf_genome_to_cdna_fasta.pl
+libexec/transdecoder/cufflinks_gtf_to_alignment_gff3.pl
+libexec/transdecoder/cufflinks_gtf_to_bed.pl
+libexec/transdecoder/extract_FL_subset.pl
+libexec/transdecoder/ffindex_resume.pl
+libexec/transdecoder/gene_list_to_gff.pl
+libexec/transdecoder/get_FL_accs.pl
+libexec/transdecoder/get_longest_ORF_per_transcript.pl
+libexec/transdecoder/get_top_longest_fasta_entries.pl
+libexec/transdecoder/gff3_file_to_bed.pl
+libexec/transdecoder/gff3_file_to_proteins.pl
+libexec/transdecoder/index_gff3_files_by_isoform.pl
+libexec/transdecoder/nr_ORFs_gff3.pl
+libexec/transdecoder/pfam_runner.pl
+libexec/transdecoder/remove_eclipsed_ORFs.pl
+libexec/transdecoder/score_CDS_liklihood_all_6_frames.pl
+libexec/transdecoder/seq_n_baseprobs_to_logliklihood_vals.pl