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Port details
bio-mocha Bcftools plugin for mosaic chromosomal alteration analysis
1.14_1 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 1.13_1Version 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: 2022-02-26 15:04:10
Commit Hash: f46ddab
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (15 items)
Collapse this list.
  1. /usr/local/share/licenses/bio-mocha-1.14_1/catalog.mk
  2. /usr/local/share/licenses/bio-mocha-1.14_1/LICENSE
  3. /usr/local/share/licenses/bio-mocha-1.14_1/MIT
  4. libexec/bcftools/extendFMT.so
  5. libexec/bcftools/mocha.so
  6. libexec/bcftools/mochatools.so
  7. libexec/bcftools/score.so
  8. libexec/bcftools/trio-phase.so
  9. share/bio-mocha/assoc_plot.R
  10. share/bio-mocha/mocha_plot.R
  11. share/bio-mocha/pileup_plot.R
  12. share/bio-mocha/summary_plot.R
  13. @owner
  14. @group
  15. @mode
Collapse this list.
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
PKGNAME: bio-mocha
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
bio-mocha
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-1.14_1
FreeBSD:12:amd641.14_11.14_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3861.14_11.14_1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch641.14_11.14_1
FreeBSD:13:amd641.14_11.14_1
FreeBSD:13:armv6-1.14_1
FreeBSD:13:armv7-1.14_1
FreeBSD:13:i3861.14_11.14_1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch641.14_1-
FreeBSD:14:amd641.14_1-
FreeBSD:14:armv61.14_1-
FreeBSD:14:armv71.14_1-
FreeBSD:14:i3861.14_1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
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>=2.69 : devel/autoconf
  4. automake>=1.16.1 : devel/automake
Runtime dependencies:
  1. bcftools>=1.14 : biology/bcftools
Library dependencies:
  1. libhts.so : biology/htslib
There are no ports dependent upon this port
Configuration Options:
Options name:
USES:
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/1.15?dummy=/
  2. https://software.broadinstitute.org/software/mocha/
Collapse this list.

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Feb 2022 15:04:10
 files touched by this commit commit hash:f46ddab3d69fb6cee784292be521a3aaf463aa97  1.14_1
 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bio-mocha: Update bcftools submodule to 1.15

Compatibility confirmed with upstream
13 Jan 2022 19:00:41
 files touched by this commit commit hash:e33f72037a797431e5c4d89d1d222c5d5d92eb27  1.14
 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bio-mocha: Update to 1.14-20220112

Upstream incorporated my patches to eliminate nested functions, which
are not standard C and pose security risks.
A few other minor updated.
21 Dec 2021 16:17:11
 files touched by this commit commit hash:7a9f4b317a0a8eecc36ef8877412eb697b937a60  1.13_1
 Jason W. Bacon (jwb) search for other commits by this committer 
bio-mocha: Build plugin against bcftools 1.14, the current port
03 Dec 2021 13:41:26
 files touched by this commit commit hash:9152cfc775fca98435610da5faad6d56c5cdeacb  1.13
 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bio-mocha: bcftools plugin for mosaic chromosomal alterations

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.

Number of commits found: 4
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