| Port details |
- bamtools API and toolkit for handling BAM files
- 2.5.2_2 biology
 =2      2.5.2_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2018-03-28 13:26:48
- Last Update: 2024-09-12 16:20:06
- Commit Hash: a63bcef
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://github.com/pezmaster31/bamtools
- Description:
- BamTools provides both a programmer's API and an end-user's toolkit for
handling BAM files.
BAM is the binary alternative to the sequence alignment/map (SAM) format used
for storing genetic sequence data. It uses BGZF block compression implemented
on top of the standard gzip file format to provide good compression while
allowing efficient random access for indexed queries.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- bamtools>0:biology/bamtools
- To install the port:
- cd /usr/ports/biology/bamtools/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/bamtools
- pkg install bamtools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: bamtools
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1625529459
SHA256 (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8
SIZE (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 245729
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:
-
- cmake : devel/cmake-core
- ninja : devel/ninja
- Library dependencies:
-
- libjsoncpp.so : devel/jsoncpp
- This port is required by:
- for Libraries
-
- biology/augustus
- for Run
-
- biology/biostar-tools
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_bamtools
- USES:
- cmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.5.2_2
12 Sep 2024 16:20:06
 |
Yuri Victorovich (yuri) |
*/*: Bump dependencioes after devel/jsoncpp update
PR: 281462
Reported by: Ale <discipline@tiscali.it> |
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) |
2.5.2_1
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  ) |
2.5.2_1
05 Nov 2021 19:09:19
|
Yuri Victorovich (yuri)
Author: Daniel Engberg |
devel/jsoncpp: Update to 1.9.4 -> 1.9.5
PR: 259654 |
2.5.2
06 Jul 2021 18:10:54
|
Jason W. Bacon (jwb) |
biology/bamtools: Update to 2.5.2
Code clean up
Changes: https://github.com/pezmaster31/bamtools/releases/tag/v2.5.2
Reported by: portscout |
2.5.1_2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.5.1_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.5.1_2
30 Jun 2020 17:46:18
 |
tcberner |
Bump devel/jsoncpp consumers after r540853.
Reported by: Kevin Oberman <rkoberman@gmail.com> |
2.5.1_1
13 Jan 2020 21:38:36
|
yuri |
devel/jsoncpp: Update 1.8.1 -> 1.9.2
PR: 229677
Differential Revision: D22905 |
2.5.1
25 Dec 2018 20:25:40
|
tcberner |
Change cmake default behaviour to outsource.
Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine |
2.5.1
28 Mar 2018 13:26:31
|
jwb |
biology/bamtools: API and toolkit for handling BAM files
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D14877 |
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