Date: Mon, 12 Dec 2022 17:30:01 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8e926be18e0a - main - biology/rna-seq: Metaport for RNA-Seq analysis Message-ID: <202212121730.2BCHU1Lw017735@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22 commit 8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2022-12-12 17:29:36 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2022-12-12 17:30:00 +0000 biology/rna-seq: Metaport for RNA-Seq analysis Metaport to install tools for typical RNA-Seq analysis, including QC, adapter trimming, alignment, and differential analysis. --- biology/Makefile | 1 + biology/rna-seq/Makefile | 26 ++++++++++++++++++++++++++ biology/rna-seq/distinfo | 1 + biology/rna-seq/pkg-descr | 2 ++ 4 files changed, 30 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index b544cbf16e59..b466435210cf 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -190,6 +190,7 @@ SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine + SUBDIR += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables diff --git a/biology/rna-seq/Makefile b/biology/rna-seq/Makefile new file mode 100644 index 000000000000..bdba35652327 --- /dev/null +++ b/biology/rna-seq/Makefile @@ -0,0 +1,26 @@ +PORTNAME= rna-seq +DISTVERSION= 0.1.0 +CATEGORIES= biology python +MASTER_SITES= # empty + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Metaport for RNA-Seq analysis +WWW= https://example.com/rna-seq + +LICENSE= BSD2CLAUSE + +RUN_DEPENDS= sra-tools>0:biology/sra-tools \ + fastq-trim>0:biology/fastq-trim \ + fastqc>0:biology/fastqc \ + ${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR} \ + biolibc-tools>0:biology/biolibc-tools \ + gffread>0:biology/gffread \ + kallisto>0:biology/kallisto \ + hisat2>0:biology/hisat2 \ + samtools>0:biology/samtools \ + igv>0:biology/igv \ + fasda>0:biology/fasda + +USES= metaport python + +.include <bsd.port.mk> diff --git a/biology/rna-seq/distinfo b/biology/rna-seq/distinfo new file mode 100644 index 000000000000..46e828c40768 --- /dev/null +++ b/biology/rna-seq/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1665354692 diff --git a/biology/rna-seq/pkg-descr b/biology/rna-seq/pkg-descr new file mode 100644 index 000000000000..f6986df491fc --- /dev/null +++ b/biology/rna-seq/pkg-descr @@ -0,0 +1,2 @@ +Metaport to install tools for typical RNA-Seq analysis, including QC, +adapter trimming, alignment, and differential analysis.
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