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Port details
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)
Collapse this list.
  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
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
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/
Collapse this list.

Number of commits found: 7

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.16
05 Jan 2023 23:21:03
commit hash: 09c70c7488989b1a37f4da6a447871c5bea06ee0commit hash: 09c70c7488989b1a37f4da6a447871c5bea06ee0commit hash: 09c70c7488989b1a37f4da6a447871c5bea06ee0commit hash: 09c70c7488989b1a37f4da6a447871c5bea06ee0 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bio-mocha: Update to 1.16

New release to sync with bcftools

Changes: https://github.com/freeseek/mocha/commits/master
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.14_1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.14_1
26 Feb 2022 15:04:10
commit hash: f46ddab3d69fb6cee784292be521a3aaf463aa97commit hash: f46ddab3d69fb6cee784292be521a3aaf463aa97commit hash: f46ddab3d69fb6cee784292be521a3aaf463aa97commit hash: f46ddab3d69fb6cee784292be521a3aaf463aa97 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bio-mocha: Update bcftools submodule to 1.15

Compatibility confirmed with upstream
1.14
13 Jan 2022 19:00:41
commit hash: e33f72037a797431e5c4d89d1d222c5d5d92eb27commit hash: e33f72037a797431e5c4d89d1d222c5d5d92eb27commit hash: e33f72037a797431e5c4d89d1d222c5d5d92eb27commit hash: e33f72037a797431e5c4d89d1d222c5d5d92eb27 files touched by this commit		 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.
1.13_1
21 Dec 2021 16:17:11
commit hash: 7a9f4b317a0a8eecc36ef8877412eb697b937a60commit hash: 7a9f4b317a0a8eecc36ef8877412eb697b937a60commit hash: 7a9f4b317a0a8eecc36ef8877412eb697b937a60commit hash: 7a9f4b317a0a8eecc36ef8877412eb697b937a60 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
bio-mocha: Build plugin against bcftools 1.14, the current port
1.13
03 Dec 2021 13:41:26
commit hash: 9152cfc775fca98435610da5faad6d56c5cdeacbcommit hash: 9152cfc775fca98435610da5faad6d56c5cdeacbcommit hash: 9152cfc775fca98435610da5faad6d56c5cdeacbcommit hash: 9152cfc775fca98435610da5faad6d56c5cdeacb files touched by this commit		 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: 7
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