From owner-svn-ports-head@freebsd.org Wed Mar 16 20:12:34 2016 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 50075AD2F82; Wed, 16 Mar 2016 20:12:34 +0000 (UTC) (envelope-from pi@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 0E5A01D5E; Wed, 16 Mar 2016 20:12:33 +0000 (UTC) (envelope-from pi@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u2GKCXCd003313; Wed, 16 Mar 2016 20:12:33 GMT (envelope-from pi@FreeBSD.org) Received: (from pi@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u2GKCWN5003308; Wed, 16 Mar 2016 20:12:32 GMT (envelope-from pi@FreeBSD.org) Message-Id: <201603162012.u2GKCWN5003308@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: pi set sender to pi@FreeBSD.org using -f From: Kurt Jaeger Date: Wed, 16 Mar 2016 20:12:32 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r411246 - in head/biology: . p5-transdecoder X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 16 Mar 2016 20:12:34 -0000 Author: pi Date: Wed Mar 16 20:12:32 2016 New Revision: 411246 URL: https://svnweb.freebsd.org/changeset/ports/411246 Log: 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 Added: head/biology/p5-transdecoder/ head/biology/p5-transdecoder/Makefile (contents, props changed) head/biology/p5-transdecoder/distinfo (contents, props changed) head/biology/p5-transdecoder/pkg-descr (contents, props changed) head/biology/p5-transdecoder/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Mar 16 19:46:35 2016 (r411245) +++ head/biology/Makefile Wed Mar 16 20:12:32 2016 (r411246) @@ -65,6 +65,7 @@ SUBDIR += p5-Bio-SCF SUBDIR += p5-bioperl SUBDIR += p5-bioperl-run + SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred Added: head/biology/p5-transdecoder/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-transdecoder/Makefile Wed Mar 16 20:12:32 2016 (r411246) @@ -0,0 +1,47 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +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 Added: head/biology/p5-transdecoder/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-transdecoder/distinfo Wed Mar 16 20:12:32 2016 (r411246) @@ -0,0 +1,2 @@ +SHA256 (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24 +SIZE (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 11500688 Added: head/biology/p5-transdecoder/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-transdecoder/pkg-descr Wed Mar 16 20:12:32 2016 (r411246) @@ -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/ Added: head/biology/p5-transdecoder/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-transdecoder/pkg-plist Wed Mar 16 20:12:32 2016 (r411246) @@ -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