From a11fc4771c87c8c76e46fda4e85b0bef9cd8cde8 Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Thu, 24 Oct 2024 08:32:05 -0500 Subject: [PATCH] biology/mca-calling: Core tools for mCA event calling 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. --- biology/Makefile | 1 + biology/mca-calling/Makefile | 27 +++++++++++++++++++++++++++ biology/mca-calling/distinfo | 1 + biology/mca-calling/pkg-descr | 5 +++++ 4 files changed, 34 insertions(+) create mode 100644 biology/mca-calling/Makefile create mode 100644 biology/mca-calling/distinfo create mode 100644 biology/mca-calling/pkg-descr diff --git a/biology/Makefile b/biology/Makefile index 192c77a0d63f..3f12e044804a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -108,6 +108,7 @@ SUBDIR += mafft SUBDIR += mapm3 SUBDIR += mashmap + SUBDIR += mca-calling SUBDIR += megahit SUBDIR += metaeuk SUBDIR += migrate diff --git a/biology/mca-calling/Makefile b/biology/mca-calling/Makefile new file mode 100644 index 000000000000..5f2afd08795f --- /dev/null +++ b/biology/mca-calling/Makefile @@ -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 diff --git a/biology/mca-calling/distinfo b/biology/mca-calling/distinfo new file mode 100644 index 000000000000..d649a5847c66 --- /dev/null +++ b/biology/mca-calling/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1729776668 diff --git a/biology/mca-calling/pkg-descr b/biology/mca-calling/pkg-descr new file mode 100644 index 000000000000..23486297ac55 --- /dev/null +++ b/biology/mca-calling/pkg-descr @@ -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.