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biology/mca-calling: Core tools for mCA event calling

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The mca-calling meta-port provides the core tools needed for performing
a typical mCA (Mosaic Chromosomal Alteration) analysis, including
conversion of SRA VCF files to a format suitable for haplohseq and
MoCha, and haplohseq and MoCha event calling.  The GWAS analysis that
follows is typically done with R-based tools installed within R.
This commit is contained in:
Jason W. Bacon 2024-10-24 08:32:05 -05:00
parent c111c96bdc
commit a11fc4771c
4 changed files with 34 additions and 0 deletions
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1
biology/Makefile
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@ -108,6 +108,7 @@
SUBDIR += mafft
SUBDIR += mapm3
SUBDIR += mashmap
SUBDIR += mca-calling
SUBDIR += megahit
SUBDIR += metaeuk
SUBDIR += migrate

27
biology/mca-calling/Makefile Normal file
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@ -0,0 +1,27 @@
PORTNAME= mca-calling
DISTVERSION= 0.1.0
CATEGORIES= biology
MASTER_SITES= # empty
MAINTAINER= jwb@FreeBSD.org
COMMENT= Core tools for Mosaic Chromosomal Alteration event calling
WWW= https://github.com/auerlab/
LICENSE= BSD2CLAUSE
RUN_DEPENDS+= sra-tools>0:biology/sra-tools
RUN_DEPENDS+= bcftools>0:biology/bcftools
RUN_DEPENDS+= samtools>0:biology/samtools
RUN_DEPENDS+= vcf-split>0:biology/vcf-split
RUN_DEPENDS+= ad2vcf>0:biology/ad2vcf
RUN_DEPENDS+= vcf2hap>0:biology/vcf2hap
RUN_DEPENDS+= haplohseq>0:biology/haplohseq
RUN_DEPENDS+= bio-mocha>0:biology/bio-mocha
RUN_DEPENDS+= bedtools>0:biology/bedtools
RUN_DEPENDS+= mawk>0:lang/mawk
RUN_DEPENDS+= curl>0:ftp/curl
RUN_DEPENDS+= liblz4>0:archivers/liblz4
USES= metaport
.include <bsd.port.mk>

1
biology/mca-calling/distinfo Normal file
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@ -0,0 +1 @@
TIMESTAMP = 1729776668

5
biology/mca-calling/pkg-descr Normal file
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@ -0,0 +1,5 @@
The mca-calling meta-port provides the core tools needed for performing
a typical mCA (Mosaic Chromosomal Alteration) analysis, including
conversion of SRA VCF files to a format suitable for haplohseq and
MoCha, and haplohseq and MoCha event calling. The GWAS analysis that
follows is typically done with R-based tools installed within R.