| Port details |
- mca-calling Core tools for Mosaic Chromosomal Alteration event calling
- 0.1.0 biology
 =0      Package not present on quarterly.This port was created during this quarter. It will be in the next quarterly branch but not the current one. - Maintainer: jwb@FreeBSD.org
- Port Added: 2024-10-24 13:33:04
- Last Update: 2024-10-24 13:32:05
- Commit Hash: a11fc47
- License: NA
- WWW:
- https://github.com/auerlab/
- Description:
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- mca-calling>0:biology/mca-calling
- To install the port:
- cd /usr/ports/biology/mca-calling/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/mca-calling
- pkg install mca-calling
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: mca-calling
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1729776668
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Runtime dependencies:
-
- sra-tools>0 : biology/sra-tools
- bcftools>0 : biology/bcftools
- samtools>0 : biology/samtools
- vcf-split>0 : biology/vcf-split
- ad2vcf>0 : biology/ad2vcf
- vcf2hap>0 : biology/vcf2hap
- haplohseq>0 : biology/haplohseq
- bio-mocha>0 : biology/bio-mocha
- bedtools>0 : biology/bedtools
- mawk>0 : lang/mawk
- curl>0 : ftp/curl
- liblz4>0 : archivers/liblz4
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_mca-calling
- USES:
- metaport
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
- There is no master site for this port.
|
Number of commits found: 1
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.1.0
24 Oct 2024 13:32:05
 |
Jason W. Bacon (jwb) |
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. |
Number of commits found: 1
|
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