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Port details on branch 2022Q3
bio-mocha Bcftools plugin for mosaic chromosomal alteration analysis
1.16 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.16Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-12-03 13:45:06
Last Update: 2023-01-05 23:21:03
Commit Hash: 09c70c7
License: MIT
WWW:
https://software.broadinstitute.org/software/mocha/
Description:
MoChA is a bcftools plugin released under the MIT license for mosaic chromosomal alteration detection and analysis from DNA microarray or whole genome sequence data. It can be used both with Illumina and Affymetrix data. It can also be used for detection of germline copy number variants. Data can be prepared in usable file formats using the gtc2vcf plugin.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (13 items)
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  1. /usr/local/share/licenses/bio-mocha-1.16/catalog.mk
  2. /usr/local/share/licenses/bio-mocha-1.16/LICENSE
  3. /usr/local/share/licenses/bio-mocha-1.16/MIT
  4. libexec/bcftools/extendFMT.so
  5. libexec/bcftools/mocha.so
  6. libexec/bcftools/mochatools.so
  7. libexec/bcftools/trio-phase.so
  8. share/bio-mocha/mocha_plot.R
  9. share/bio-mocha/pileup_plot.R
  10. share/bio-mocha/summary_plot.R
  11. @owner
  12. @group
  13. @mode
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Dependency lines:
  • bio-mocha>0:biology/bio-mocha
To install the port:
cd /usr/ports/biology/bio-mocha/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bio-mocha
  • pkg install bio-mocha
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bio-mocha
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1672095342 SHA256 (bio-mocha_1.16-20221221.tar.gz) = 576cbdda53760f353fc8fd989751716b1d4f8c5e1921f838c263476282cced86 SIZE (bio-mocha_1.16-20221221.tar.gz) = 68625

Expand this list (2 items)

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SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3 SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435

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Packages (timestamps in pop-ups are UTC):
bio-mocha
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.161.16-1.161.16---
FreeBSD:13:quarterly1.161.161.161.161.161.161.161.16
FreeBSD:14:latest1.161.161.161.161.161.16-1.16
FreeBSD:14:quarterly1.161.16-1.161.161.161.161.16
FreeBSD:15:latest1.161.16n/a1.16n/a1.161.161.16
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. gmake>=4.3 : devel/gmake
  3. autoconf>=2.71 : devel/autoconf
  4. automake>=1.16.5 : devel/automake
Test dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. bcftools>=1.16 : biology/bcftools
Library dependencies:
  1. libhts.so : biology/htslib
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_bio-mocha
USES:
autoreconf gmake localbase perl5 python:env shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://codeload.github.com/samtools/bcftools/tar.gz/1.16?dummy=/
  2. https://software.broadinstitute.org/software/mocha/
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There are no commits on branch 2022Q3 for this port
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