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| author | jwb <jwb@FreeBSD.org> | 2017-12-09 21:23:32 +0800 |
|---|---|---|
| committer | jwb <jwb@FreeBSD.org> | 2017-12-09 21:23:32 +0800 |
| commit | 69eb1c930bacc61b86feb40b592052d0b7e5882c (patch) | |
| tree | 787e8f01a0cf448674d567c4465af566b2a8e47c /biology/p5-TrimGalore | |
| parent | 09c6f9094f9c760773a4c04cface8bae5b89841f (diff) | |
| download | freebsd-ports-gnome-69eb1c930bacc61b86feb40b592052d0b7e5882c.tar.gz freebsd-ports-gnome-69eb1c930bacc61b86feb40b592052d0b7e5882c.tar.zst freebsd-ports-gnome-69eb1c930bacc61b86feb40b592052d0b7e5882c.zip | |
[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming
Approved by: jrm (mentor)
Differential Revision: D13400
Diffstat (limited to 'biology/p5-TrimGalore')
| -rw-r--r-- | biology/p5-TrimGalore/Makefile | 31 | ||||
| -rw-r--r-- | biology/p5-TrimGalore/distinfo | 3 | ||||
| -rw-r--r-- | biology/p5-TrimGalore/pkg-descr | 4 | ||||
| -rw-r--r-- | biology/p5-TrimGalore/pkg-plist | 8 |
4 files changed, 46 insertions, 0 deletions
diff --git a/biology/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile new file mode 100644 index 000000000000..2121137a66a4 --- /dev/null +++ b/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> diff --git a/biology/p5-TrimGalore/distinfo b/biology/p5-TrimGalore/distinfo new file mode 100644 index 000000000000..2b718e79b72d --- /dev/null +++ b/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 diff --git a/biology/p5-TrimGalore/pkg-descr b/biology/p5-TrimGalore/pkg-descr new file mode 100644 index 000000000000..849448684845 --- /dev/null +++ b/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 diff --git a/biology/p5-TrimGalore/pkg-plist b/biology/p5-TrimGalore/pkg-plist new file mode 100644 index 000000000000..a9fa63919c1f --- /dev/null +++ b/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 |