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[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming

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Approved by: jrm (mentor)
Differential Revision:	D13400
This commit is contained in:
Jason W. Bacon 2017-12-09 13:23:32 +00:00
parent 01a822b6a0
commit 7b14021ad6
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=455857
5 changed files with 47 additions and 0 deletions
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1
biology/Makefile
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@ -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

31
biology/p5-TrimGalore/Makefile Normal file
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@ -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>

3
biology/p5-TrimGalore/distinfo Normal file
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@ -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

4
biology/p5-TrimGalore/pkg-descr Normal file
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@ -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

8
biology/p5-TrimGalore/pkg-plist Normal file
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@ -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