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D13400.id36338.diff
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D13400.id36338.diff

Index: biology/p5-trimgalore/Makefile
===================================================================
--- /dev/null
+++ biology/p5-trimgalore/Makefile
@@ -0,0 +1,31 @@
+# $FreeBSD$
+
+PORTNAME= TrimGalore
+DISTVERSION= 0.4.5
+CATEGORIES= biology perl5
+PKGNAMEPREFIX= p5-
+
+MAINTAINER= jwb@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>
Index: biology/p5-trimgalore/distinfo
===================================================================
--- /dev/null
+++ biology/p5-trimgalore/distinfo
@@ -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
Index: biology/p5-trimgalore/pkg-descr
===================================================================
--- /dev/null
+++ biology/p5-trimgalore/pkg-descr
@@ -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
Index: biology/p5-trimgalore/pkg-plist
===================================================================
--- /dev/null
+++ biology/p5-trimgalore/pkg-plist
@@ -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

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