[new port] biology/fastqc: Quality control tool for high throughput sequence data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13304

4 files changed, 259 insertions, 0 deletions

diff --git a/biology/fastqc/Makefile b/biology/fastqc/Makefile
new file mode 100644
index 000000000000..49fcd206356c
--- /dev/null
+++ b/biology/fastqc/Makefile
@@ -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>
diff --git a/biology/fastqc/distinfo b/biology/fastqc/distinfo
new file mode 100644
index 000000000000..df179e654f3f
--- /dev/null
+++ b/biology/fastqc/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1509737655
+SHA256 (fastqc_v0.11.5.zip) = dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66
+SIZE (fastqc_v0.11.5.zip) = 10026429
diff --git a/biology/fastqc/pkg-descr b/biology/fastqc/pkg-descr
new file mode 100644
index 000000000000..4ee7f74214dd
--- /dev/null
+++ b/biology/fastqc/pkg-descr
@@ -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/
diff --git a/biology/fastqc/pkg-plist b/biology/fastqc/pkg-plist
new file mode 100644
index 000000000000..ffbb0338d11e
--- /dev/null
+++ b/biology/fastqc/pkg-plist
@@ -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 Modules/per_base_quality.png
+%%DATADIR%%/Help/3 Analysis Modules/per_base_sequence_content.png
+%%DATADIR%%/Help/3 Analysis Modules/per_sequence_gc_content.png
+%%DATADIR%%/Help/3 Analysis Modules/per_sequence_quality.png
+%%DATADIR%%/Help/3 Analysis Modules/per_tile_quality.png
+%%DATADIR%%/Help/3 Analysis Modules/sequence_length_distribution.png
+%%DATADIR%%/Templates/Icons/error.png
+%%DATADIR%%/Templates/Icons/fastqc_icon.png
+%%DATADIR%%/Templates/Icons/tick.png
+%%DATADIR%%/Templates/Icons/warning.png
+%%DATADIR%%/Templates/fastqc2fo.xsl
+%%DATADIR%%/Templates/header_template.html
+%%JAVAJARDIR%%/fastqc/cisd-jhdf5.jar
+%%JAVAJARDIR%%/fastqc/jbzip2-0.9.jar
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+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/UnivariateFunction.class
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