svn commit: r455857 - in head/biology: . p5-TrimGalore

[Jason W. Bacon]

Author: jwb
Date: Sat Dec  9 13:23:32 2017
New Revision: 455857
URL: https://svnweb.freebsd.org/changeset/ports/455857

Log:
  [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming
  Approved by: jrm (mentor)
  Differential Revision:	D13400

Added:
  head/biology/p5-TrimGalore/
  head/biology/p5-TrimGalore/Makefile   (contents, props changed)
  head/biology/p5-TrimGalore/distinfo   (contents, props changed)
  head/biology/p5-TrimGalore/pkg-descr   (contents, props changed)
  head/biology/p5-TrimGalore/pkg-plist   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sat Dec  9 13:12:12 2017	(r455856)
+++ head/biology/Makefile	Sat Dec  9 13:23:32 2017	(r455857)
@@ -73,6 +73,7 @@
     SUBDIR += p5-Bio-SCF
     SUBDIR += p5-BioPerl
     SUBDIR += p5-BioPerl-Run
+    SUBDIR += p5-TrimGalore
     SUBDIR += p5-transdecoder
     SUBDIR += paml
     SUBDIR += phrap

Added: head/biology/p5-TrimGalore/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-TrimGalore/Makefile	Sat Dec  9 13:23:32 2017	(r455857)
@@ -0,0 +1,31 @@
+# $FreeBSD$
+
+PORTNAME=	TrimGalore
+DISTVERSION=	0.4.5
+CATEGORIES=	biology perl5
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Wrapper around Cutadapt and FastQC for adapter and quality trimming
+
+LICENSE=	GPLv3
+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:env shebangfix
+SHEBANG_FILES=	trim_galore
+USE_PERL5=	run
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	FelixKrueger
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/trim_galore ${STAGEDIR}${PREFIX}/bin
+	cd ${WRKSRC} && ${COPYTREE_SHARE} test_files ${STAGEDIR}${DATADIR}
+
+.include <bsd.port.mk>

Added: head/biology/p5-TrimGalore/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-TrimGalore/distinfo	Sat Dec  9 13:23:32 2017	(r455857)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1512570215
+SHA256 (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c
+SIZE (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = 21983909

Added: head/biology/p5-TrimGalore/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-TrimGalore/pkg-descr	Sat Dec  9 13:23:32 2017	(r455857)
@@ -0,0 +1,4 @@
+Wrapper around Cutadapt and FastQC to consistently apply adapter and quality
+trimming to FastQ files, with extra functionality for RRBS data.
+
+WWW: https://github.com/FelixKrueger/TrimGalore

Added: head/biology/p5-TrimGalore/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-TrimGalore/pkg-plist	Sat Dec  9 13:23:32 2017	(r455857)
@@ -0,0 +1,8 @@
+bin/trim_galore
+%%DATADIR%%/test_files/4_seqs_with_Ns.fastq.gz
+%%DATADIR%%/test_files/colorspace_file.fastq
+%%DATADIR%%/test_files/empty_file.fastq
+%%DATADIR%%/test_files/illumina_100K.fastq.gz
+%%DATADIR%%/test_files/nextera_100K.fastq.gz
+%%DATADIR%%/test_files/smallRNA_100K.fastq.gz
+%%DATADIR%%/test_files/truncated.fq.gz