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Bacon" Date: Tue, 23 Oct 2018 12:51:20 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r482836 - head/biology/p5-transdecoder X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: head/biology/p5-transdecoder X-SVN-Commit-Revision: 482836 X-SVN-Commit-Repository: ports 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: 2.1.29 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: Tue, 23 Oct 2018 12:51:22 -0000 Author: jwb Date: Tue Oct 23 12:51:20 2018 New Revision: 482836 URL: https://svnweb.freebsd.org/changeset/ports/482836 Log: biology/p5-transdecoder: Upgrade to 5.4.0 Minor clean up to silence portlint Approved by: jrm (mentor, implicit) Modified: head/biology/p5-transdecoder/Makefile head/biology/p5-transdecoder/distinfo head/biology/p5-transdecoder/pkg-descr head/biology/p5-transdecoder/pkg-plist Modified: head/biology/p5-transdecoder/Makefile ============================================================================== --- head/biology/p5-transdecoder/Makefile Tue Oct 23 12:32:59 2018 (r482835) +++ head/biology/p5-transdecoder/Makefile Tue Oct 23 12:51:20 2018 (r482836) @@ -1,9 +1,8 @@ # $FreeBSD$ PORTNAME= transdecoder -PORTVERSION= 2.1.0 -PORTREVISION= 1 -DISTVERSIONPREFIX=v +DISTVERSIONPREFIX= TransDecoder-v +DISTVERSION= 5.4.0 CATEGORIES= biology perl5 PKGNAMEPREFIX= p5- @@ -15,31 +14,35 @@ LICENSE= BSD3CLAUSE RUN_DEPENDS= cd-hit>=4.6.1:biology/cd-hit \ p5-URI>0:net/p5-URI -NO_BUILD= yes -NO_ARCH= yes USES= perl5 shebangfix +USE_GITHUB= yes + +GH_PROJECT= TransDecoder 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 +NO_BUILD= yes +NO_ARCH= yes PERL_MOD_DIR= ${PREFIX}/${SITE_PERL_REL}/${PORTNAME} PERL_UTIL_DIR= ${PREFIX}/libexec/${PORTNAME} +SCRIPTS= ${WRKSRC}/TransDecoder.LongOrfs \ + ${WRKSRC}/TransDecoder.Predict post-patch: - ${REINPLACE_CMD} \ + @${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 + ${SCRIPTS} \ + ${WRKSRC}/util/*.pl do-install: - ${MKDIR} ${STAGEDIR}${PERL_MOD_DIR} ${STAGEDIR}${PERL_UTIL_DIR} + @${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} ${SCRIPTS} ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl ${STAGEDIR}${PERL_UTIL_DIR} .include Modified: head/biology/p5-transdecoder/distinfo ============================================================================== --- head/biology/p5-transdecoder/distinfo Tue Oct 23 12:32:59 2018 (r482835) +++ head/biology/p5-transdecoder/distinfo Tue Oct 23 12:51:20 2018 (r482836) @@ -1,2 +1,3 @@ -SHA256 (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24 -SIZE (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 11500688 +TIMESTAMP = 1540225907 +SHA256 (transdecoder-TransDecoder-TransDecoder-v5.4.0_GH0.tar.gz) = a6fa776c6eac30922632df1a5362b7564bfcb05728daeb53d0c2c3a9dc899df5 +SIZE (transdecoder-TransDecoder-TransDecoder-v5.4.0_GH0.tar.gz) = 15748557 Modified: head/biology/p5-transdecoder/pkg-descr ============================================================================== --- head/biology/p5-transdecoder/pkg-descr Tue Oct 23 12:32:59 2018 (r482835) +++ head/biology/p5-transdecoder/pkg-descr Tue Oct 23 12:51:20 2018 (r482836) @@ -1,6 +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. +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/ Modified: head/biology/p5-transdecoder/pkg-plist ============================================================================== --- head/biology/p5-transdecoder/pkg-plist Tue Oct 23 12:32:59 2018 (r482835) +++ head/biology/p5-transdecoder/pkg-plist Tue Oct 23 12:51:20 2018 (r482836) @@ -1,22 +1,23 @@ bin/TransDecoder.LongOrfs -bin/TransDecoder.LongOrfs.bak bin/TransDecoder.Predict -bin/TransDecoder.Predict.bak +%%SITE_PERL%%/transdecoder/DelimParser.pm %%SITE_PERL%%/transdecoder/Fasta_reader.pm %%SITE_PERL%%/transdecoder/Fasta_retriever.pm -%%SITE_PERL%%/transdecoder/GFF3_utils.pm +%%SITE_PERL%%/transdecoder/GFF3_utils2.pm +%%SITE_PERL%%/transdecoder/GTF.pm +%%SITE_PERL%%/transdecoder/GTF_utils2.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 +%%SITE_PERL%%/transdecoder/Overlap_piler.pm +%%SITE_PERL%%/transdecoder/PWM.pm +%%SITE_PERL%%/transdecoder/Pipeliner.pm +%%SITE_PERL%%/transdecoder/Process_cmd.pm +%%SITE_PERL%%/transdecoder/overlapping_nucs.ph 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/exclude_similar_proteins.pl +libexec/transdecoder/fasta_prot_checker.pl libexec/transdecoder/ffindex_resume.pl libexec/transdecoder/gene_list_to_gff.pl libexec/transdecoder/get_FL_accs.pl @@ -24,9 +25,18 @@ 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/gff3_gene_to_gtf_format.pl +libexec/transdecoder/gtf_genome_to_cdna_fasta.pl +libexec/transdecoder/gtf_to_alignment_gff3.pl +libexec/transdecoder/gtf_to_bed.pl libexec/transdecoder/nr_ORFs_gff3.pl libexec/transdecoder/pfam_runner.pl +libexec/transdecoder/refine_gff3_group_iso_strip_utrs.pl +libexec/transdecoder/refine_hexamer_scores.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 +libexec/transdecoder/score_CDS_likelihood_all_6_frames.pl +libexec/transdecoder/select_best_ORFs_per_transcript.pl +libexec/transdecoder/seq_n_baseprobs_to_loglikelihood_vals.pl +libexec/transdecoder/start_codon_refinement.pl +libexec/transdecoder/train_start_PWM.pl +libexec/transdecoder/uri_unescape.pl