git: a11fc4771c87 - main - biology/mca-calling: Core tools for mCA event calling
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Date: Thu, 24 Oct 2024 13:32:33 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=a11fc4771c87c8c76e46fda4e85b0bef9cd8cde8
commit a11fc4771c87c8c76e46fda4e85b0bef9cd8cde8
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-10-24 13:32:05 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-10-24 13:32:05 +0000
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(+)
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 <bsd.port.mk>
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.