Date: Sun, 24 Mar 2019 21:44:17 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r496785 - in head/biology/p5-TrimGalore: . files Message-ID: <201903242144.x2OLiHjh005161@repo.freebsd.org>
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Author: jwb Date: Sun Mar 24 21:44:17 2019 New Revision: 496785 URL: https://svnweb.freebsd.org/changeset/ports/496785 Log: biology/p5-TrimGalore: Upgrade to 0.6.1 Add test script Added: head/biology/p5-TrimGalore/files/ head/biology/p5-TrimGalore/files/trim_galore-test.in (contents, props changed) Modified: head/biology/p5-TrimGalore/Makefile head/biology/p5-TrimGalore/distinfo (contents, props changed) head/biology/p5-TrimGalore/pkg-plist (contents, props changed) Modified: head/biology/p5-TrimGalore/Makefile ============================================================================== --- head/biology/p5-TrimGalore/Makefile Sun Mar 24 21:28:02 2019 (r496784) +++ head/biology/p5-TrimGalore/Makefile Sun Mar 24 21:44:17 2019 (r496785) @@ -1,8 +1,8 @@ # $FreeBSD$ PORTNAME= TrimGalore -DISTVERSION= 0.4.5 -CATEGORIES= biology perl5 +DISTVERSION= 0.6.1 +CATEGORIES= biology perl5 python PKGNAMEPREFIX= p5- MAINTAINER= jwb@FreeBSD.org @@ -14,18 +14,21 @@ LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \ fastqc>0:biology/fastqc -NO_ARCH= yes -NO_BUILD= yes - -USES= perl5 python:3.4+,env shebangfix -SHEBANG_FILES= trim_galore +# Future: Can 3.4+ be determined from cutadapt dep? +USES= perl5 python:env,3.4+ shebangfix USE_PERL5= run - USE_GITHUB= yes + +SHEBANG_FILES= trim_galore GH_ACCOUNT= FelixKrueger +NO_ARCH= yes +NO_BUILD= yes +SUB_FILES= trim_galore-test + do-install: ${INSTALL_SCRIPT} ${WRKSRC}/trim_galore ${STAGEDIR}${PREFIX}/bin + ${INSTALL_SCRIPT} ${WRKDIR}/trim_galore-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC} && ${COPYTREE_SHARE} test_files ${STAGEDIR}${DATADIR} .include <bsd.port.mk> Modified: head/biology/p5-TrimGalore/distinfo ============================================================================== --- head/biology/p5-TrimGalore/distinfo Sun Mar 24 21:28:02 2019 (r496784) +++ head/biology/p5-TrimGalore/distinfo Sun Mar 24 21:44:17 2019 (r496785) @@ -1,3 +1,3 @@ -TIMESTAMP = 1512570215 -SHA256 (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c -SIZE (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = 21983909 +TIMESTAMP = 1553345061 +SHA256 (FelixKrueger-TrimGalore-0.6.1_GH0.tar.gz) = 658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0 +SIZE (FelixKrueger-TrimGalore-0.6.1_GH0.tar.gz) = 26825390 Added: head/biology/p5-TrimGalore/files/trim_galore-test.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-TrimGalore/files/trim_galore-test.in Sun Mar 24 21:44:17 2019 (r496785) @@ -0,0 +1,13 @@ +#!/bin/sh + +test_dir=%%DATADIR%%/test_files +for file in $test_dir/*.fastq.gz $test_dir/*.fq.gz; do + cat << EOM + +=============================================================================== +Trimming $file... +=============================================================================== + +EOM + trim_galore $file +done Modified: head/biology/p5-TrimGalore/pkg-plist ============================================================================== --- head/biology/p5-TrimGalore/pkg-plist Sun Mar 24 21:28:02 2019 (r496784) +++ head/biology/p5-TrimGalore/pkg-plist Sun Mar 24 21:44:17 2019 (r496785) @@ -1,8 +1,20 @@ bin/trim_galore +bin/trim_galore-test %%DATADIR%%/test_files/4_seqs_with_Ns.fastq.gz +%%DATADIR%%/test_files/clock_10K_R1.fastq.gz +%%DATADIR%%/test_files/clock_10K_R2.fastq.gz %%DATADIR%%/test_files/colorspace_file.fastq %%DATADIR%%/test_files/empty_file.fastq %%DATADIR%%/test_files/illumina_100K.fastq.gz +%%DATADIR%%/test_files/illumina_100K.fastq.gz_trimming_report.txt +%%DATADIR%%/test_files/illumina_10K.fastq.gz +%%DATADIR%%/test_files/illumina_10K.fastq.gz_trimming_report.txt +%%DATADIR%%/test_files/illumina_10K_trimmed.fq.gz %%DATADIR%%/test_files/nextera_100K.fastq.gz +%%DATADIR%%/test_files/nextera_100K.fastq.gz_trimming_report.txt %%DATADIR%%/test_files/smallRNA_100K.fastq.gz +%%DATADIR%%/test_files/smallRNA_100K.fastq.gz_trimming_report.txt +%%DATADIR%%/test_files/smallRNA_100K_R1.fastq.gz_trimming_report.txt +%%DATADIR%%/test_files/smallRNA_100K_R2.fastq.gz +%%DATADIR%%/test_files/smallRNA_100K_R2.fastq.gz_trimming_report.txt %%DATADIR%%/test_files/truncated.fq.gz
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