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biology/chip-seq: Update to 1.2 

Update python versions to match py-macs2
Add sra-tools and a few commonly used archivers to metapkg
This commit is contained in:
bacon 2023-12-23 16:35:38 +00:00
parent 53208d79dc
commit c731e5bc15
2 changed files with 30 additions and 21 deletions
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11
biology/chip-seq/DESCR
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@ -1,5 +1,6 @@
The chip-seq meta-package provides the core tools needed for performing
a typical ChIP-Seq differential accessibility analysis, including
adapter trimming, quality control, alignment, peak calling, and
identification of differentially accessible peaks. Researchers may
want additional tools for data manipulation, gene ontology, etc.
The chip-seq meta-package provides the core tools needed for
performing a typical ChIP-Seq differential accessibility analysis,
including adapter trimming, quality control, alignment, peak calling,
and identification of differentially accessible peaks. Researchers
may want additional tools for data manipulation, gene ontology,
etc.

40
biology/chip-seq/Makefile
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@ -1,29 +1,37 @@
# $NetBSD: Makefile,v 1.5 2023/11/05 23:48:31 wiz Exp $
# $NetBSD: Makefile,v 1.6 2023/12/23 16:35:38 bacon Exp $
DISTNAME= chip-seq-1.1
PKGREVISION= 1
# Update minor version when adding or removing dependencies
# Update revision for all other changes
DISTNAME= chip-seq-1.2
CATEGORIES= biology meta-pkgs
MASTER_SITES= # empty
OWNER= bacon@NetBSD.org
COMMENT= Core tools needed for ChIP-Seq analysis
DEPENDS+= fastq-trim>=0:../../biology/fastq-trim
DEPENDS+= fastqc>=0:../../biology/fastqc
DEPENDS+= biolibc-tools>=0:../../biology/biolibc-tools
DEPENDS+= gffread>=0:../../biology/gffread
DEPENDS+= bwa>=0:../../biology/bwa
DEPENDS+= bowtie2>=0:../../biology/bowtie2
DEPENDS+= samtools>=0:../../biology/samtools
DEPENDS+= igv>=0:../../biology/igv
DEPENDS+= ${PYPKGPREFIX}-macs2>=0:../../biology/py-macs2
DEPENDS+= fasda>=0:../../biology/fasda
DEPENDS+= peak-classifier>=0:../../biology/peak-classifier
DEPENDS+= webbrowser>=0:../../www/webbrowser
DEPENDS+= sra-tools>0:../../biology/sra-tools
DEPENDS+= fastq-trim>0:../../biology/fastq-trim
DEPENDS+= fastqc>0:../../biology/fastqc
DEPENDS+= biolibc-tools>0:../../biology/biolibc-tools
DEPENDS+= gffread>0:../../biology/gffread
DEPENDS+= bwa>0:../../biology/bwa
DEPENDS+= bowtie2>0:../../biology/bowtie2
DEPENDS+= samtools>0:../../biology/samtools
DEPENDS+= igv>0:../../biology/igv
DEPENDS+= ${PYPKGPREFIX}-macs2>0:../../biology/py-macs2
DEPENDS+= fasda>0:../../biology/fasda
DEPENDS+= peak-classifier>0:../../biology/peak-classifier
DEPENDS+= ${PYPKGPREFIX}-multiqc-[0-9]*:../../biology/py-multiqc
DEPENDS+= webbrowser>0:../../www/webbrowser
DEPENDS+= curl>0:../../www/curl
DEPENDS+= lz4>0:../../archivers/lz4
DEPENDS+= xz>0:../../archivers/xz
DEPENDS+= zstd>0:../../archivers/zstd
META_PACKAGE= yes
PYTHON_VERSIONS_INCOMPATIBLE= 27 38 312
# Inherited from py-macs2 dep
PYTHON_VERSIONS_INCOMPATIBLE= 27 38
.include "../../lang/python/application.mk"
.include "../../mk/bsd.pkg.mk"