| Port details |
- vt Discovers short variants from Next Generation Sequencing data
- 0.57721_3 biology
 =2      0.57721_3Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2020-06-04 18:28:20
- Last Update: 2023-01-06 01:19:19
- Commit Hash: 173b9df
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://genome.sph.umich.edu/wiki/Vt
- Description:
- vt is a variant tool set that discovers short variants from Next Generation
Sequencing data.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/vt/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/vt
- pkg install vt
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: vt
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1591286057
SHA256 (atks-vt-0.57721_GH0.tar.gz) = 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17
SIZE (atks-vt-0.57721_GH0.tar.gz) = 20925247
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- Library dependencies:
-
- libhts.so : biology/htslib
- libsvm.so : science/libsvm
- libdeflate.so : archivers/libdeflate
- libcurl.so : ftp/curl
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_vt
- USES:
- compiler:c++0x gmake ssl
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 9
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.57721_3
06 Jan 2023 01:19:19
 |
Jason W. Bacon (jwb) |
biology/vt: Bump PORTREVISION for biology/htslib update |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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) |
0.57721_2
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
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  ) |
0.57721_2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.57721_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.57721_2
09 Nov 2020 00:35:58
 |
jwb |
biology/vt: Fix build with htslib 1.11
Reported by: fallout |
0.57721_1
03 Aug 2020 17:42:32
|
jwb |
biology/vt: Patch to work with htslib 1.10.2
Minor API changes requiring type casts |
0.57721
05 Jun 2020 03:49:54
|
linimon |
Add compiler:c++0x to USES to fix build on GCC-based systems:
cc1plus: error: unrecognized command line option "-std=c++0x
Approved by: portmgr (tier-2 blanket) |
0.57721
04 Jun 2020 18:28:13
|
jwb |
bioloty/vt: Discovers short variants from Next Generation Sequencing data |
Number of commits found: 9
|
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