CVS commit: pkgsrc/biology/mca-calling

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue Oct 15 12:15:29 UTC 2024

Added Files:
        pkgsrc/biology/mca-calling: DESCR Makefile

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

The mca-calling meta-package 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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/mca-calling/DESCR \
    pkgsrc/biology/mca-calling/Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/mca-calling/DESCR
diff -u /dev/null pkgsrc/biology/mca-calling/DESCR:1.1
--- /dev/null   Tue Oct 15 12:15:29 2024
+++ pkgsrc/biology/mca-calling/DESCR    Tue Oct 15 12:15:29 2024
@@ -0,0 +1,6 @@
+The mca-calling meta-package 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.
Index: pkgsrc/biology/mca-calling/Makefile
diff -u /dev/null pkgsrc/biology/mca-calling/Makefile:1.1
--- /dev/null   Tue Oct 15 12:15:29 2024
+++ pkgsrc/biology/mca-calling/Makefile Tue Oct 15 12:15:29 2024
@@ -0,0 +1,31 @@
+# $NetBSD: Makefile,v 1.1 2024/10/15 12:15:29 bacon Exp $
+#
+# Update minor version when adding/removing dependencies
+# Update revision for lesser changes
+
+DISTNAME=      mca-calling-0.1.0
+CATEGORIES=    biology meta-pkgs
+MASTER_SITES=  # empty
+
+OWNER=         bacon%NetBSD.org@localhost
+COMMENT=       Core tools for Mosaic Chromosomal Alteration event calling
+
+DEPENDS+=      sra-tools>0:../../biology/sra-tools
+DEPENDS+=      bcftools>0:../../biology/bcftools
+DEPENDS+=      samtools>0:../../biology/samtools
+DEPENDS+=      vcf-split>0:../../biology/vcf-split
+DEPENDS+=      ad2vcf>0:../../biology/ad2vcf
+DEPENDS+=      vcf2hap>0:../../biology/vcf2hap
+DEPENDS+=      haplohseq>0:../../biology/haplohseq
+DEPENDS+=      bio-mocha>0:../../biology/bio-mocha
+DEPENDS+=      bedtools>0:../../biology/bedtools
+DEPENDS+=      mawk>0:../../lang/mawk
+DEPENDS+=      curl>0:../../www/curl
+DEPENDS+=      lz4>0:../../archivers/lz4
+DEPENDS+=      bzip2>0:../../archivers/bzip2
+DEPENDS+=      xz>0:../../archivers/xz
+DEPENDS+=      zstd>0:../../archivers/zstd
+
+META_PACKAGE=  yes
+
+.include "../../mk/bsd.pkg.mk"