Date: Thu, 30 Nov 2017 22:54:29 +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: r455236 - in head/biology: . fastqc Message-ID: <201711302254.vAUMsTZd082259@repo.freebsd.org>
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Author: jwb Date: Thu Nov 30 22:54:29 2017 New Revision: 455236 URL: https://svnweb.freebsd.org/changeset/ports/455236 Log: [new port] biology/fastqc: Quality control tool for high throughput sequence data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13304 Added: head/biology/fastqc/ head/biology/fastqc/Makefile (contents, props changed) head/biology/fastqc/distinfo (contents, props changed) head/biology/fastqc/pkg-descr (contents, props changed) head/biology/fastqc/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Nov 30 22:11:04 2017 (r455235) +++ head/biology/Makefile Thu Nov 30 22:54:29 2017 (r455236) @@ -26,6 +26,7 @@ SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool + SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate Added: head/biology/fastqc/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastqc/Makefile Thu Nov 30 22:54:29 2017 (r455236) @@ -0,0 +1,43 @@ +# $FreeBSD$ + +PORTNAME= fastqc +DISTVERSIONPREFIX= v +DISTVERSION= 0.11.5 +CATEGORIES= biology java perl5 +MASTER_SITES= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +DISTNAME= ${PORTNAME}_${DISTVERSIONPREFIX}${DISTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Quality control tool for high throughput sequence data + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +NO_ARCH= yes +NO_BUILD= yes + +USES= zip perl5 shebangfix +SHEBANG_FILES= fastqc +USE_JAVA= yes +USE_PERL5= run + +WRKSRC= ${WRKDIR}/FastQC + +post-patch: + ${REINPLACE_CMD} \ + -e 's|$$RealBin$$delimiter|${DATADIR}$$delimiter${JAVAJARDIR}/fastqc$$delimiter|g' \ + -e 's|$$RealBin/|${JAVAJARDIR}/fastqc/|g' \ + ${WRKSRC}/fastqc + +# Help files are not optional docs, but required for Help menu functionality +do-install: + ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/fastqc + ${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/fastqc + ${INSTALL_SCRIPT} ${WRKSRC}/fastqc \ + ${STAGEDIR}${PREFIX}/bin + cd ${WRKSRC} && ${COPYTREE_SHARE} "Configuration Help Templates" \ + ${STAGEDIR}${DATADIR} + cd ${WRKSRC} && ${COPYTREE_SHARE} "net org uk" \ + ${STAGEDIR}${JAVAJARDIR}/fastqc + +.include <bsd.port.mk> Added: head/biology/fastqc/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastqc/distinfo Thu Nov 30 22:54:29 2017 (r455236) @@ -0,0 +1,3 @@ +TIMESTAMP = 1509737655 +SHA256 (fastqc_v0.11.5.zip) = dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66 +SIZE (fastqc_v0.11.5.zip) = 10026429 Added: head/biology/fastqc/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastqc/pkg-descr Thu Nov 30 22:54:29 2017 (r455236) @@ -0,0 +1,7 @@ +FastQC aims to provide a simple way to do some quality control checks on raw +sequence data coming from high throughput sequencing pipelines. It provides a +modular set of analyses which you can use to give a quick impression of whether +your data has any problems of which you should be aware before doing any +further analysis. + +WWW: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Added: head/biology/fastqc/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastqc/pkg-plist Thu Nov 30 22:54:29 2017 (r455236) @@ -0,0 +1,206 @@ +bin/fastqc +%%DATADIR%%/Configuration/adapter_list.txt +%%DATADIR%%/Configuration/contaminant_list.txt +%%DATADIR%%/Configuration/limits.txt +%%DATADIR%%/Help/1 Introduction/1.1 What is FastQC.html +%%DATADIR%%/Help/2 Basic Operations/2.1 Opening a sequence file.html +%%DATADIR%%/Help/2 Basic Operations/2.2 Evaluating Results.html +%%DATADIR%%/Help/2 Basic Operations/2.3 Saving a Report.html +%%DATADIR%%/Help/3 Analysis Modules/1 Basic Statistics.html +%%DATADIR%%/Help/3 Analysis Modules/10 Adapter Content.html +%%DATADIR%%/Help/3 Analysis Modules/11 Kmer Content.html +%%DATADIR%%/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html +%%DATADIR%%/Help/3 Analysis Modules/2 Per Base Sequence Quality.html +%%DATADIR%%/Help/3 Analysis Modules/3 Per Sequence Quality Scores.html +%%DATADIR%%/Help/3 Analysis Modules/4 Per Base Sequence Content.html +%%DATADIR%%/Help/3 Analysis Modules/5 Per Sequence GC Content.html +%%DATADIR%%/Help/3 Analysis Modules/6 Per Base N Content.html +%%DATADIR%%/Help/3 Analysis Modules/7 Sequence Length Distribution.html +%%DATADIR%%/Help/3 Analysis Modules/8 Duplicate Sequences.html +%%DATADIR%%/Help/3 Analysis Modules/9 Overrepresented Sequences.html +%%DATADIR%%/Help/3 Analysis Modules/duplication_levels.png +%%DATADIR%%/Help/3 Analysis Modules/kmer_profiles.png +%%DATADIR%%/Help/3 Analysis Modules/per_base_gc_content.png +%%DATADIR%%/Help/3 Analysis Modules/per_base_n_content.png +%%DATADIR%%/Help/3 Analysis 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