| Port details |
- bbmap BBMap short read aligner, and other bioinformatic tools
- 39.15 biology
 =2      38.92Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-18 16:24:08
- Last Update: 2025-01-16 12:35:49
- Commit Hash: 25e2eac
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: java
- License: BSD3CLAUSE
- WWW:
- https://jgi.doe.gov/data-and-tools/bbtools/
- https://sourceforge.net/projects/bbmap/
- https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/
- Description:
- This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
  ¦  ¦  ¦  ¦ 
- 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/bbmap/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/bbmap
- pkg install bbmap
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: bbmap
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1737030117
SHA256 (BBMap_39.15.tar.gz) = b6698469a2a90f4930537c575ff1f70332f88a933dd5e286c83ea0ff30802344
SIZE (BBMap_39.15.tar.gz) = 12498916
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Runtime dependencies:
-
- bash : shells/bash
- pigz : archivers/pigz
- pbzip2 : archivers/pbzip2
- java : java/openjdk8
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_bbmap
- USES:
- java shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 7
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
39.15
16 Jan 2025 12:35:49
 |
Jason W. Bacon (jwb) |
biology/bbmap: Update to 39.15
Add bitbucket link to WWW for some level of change tracking
Release highlights:
https://bitbucket.org/berkeleylab/jgi-bbtools/commits/branch/master
Reported by: portscout |
39.14
13 Jan 2025 21:50:59
|
Jason W. Bacon (jwb) |
biology/bbmap: Update to 39.14
Changes: Cannot find any release notes
PR: 283240
Reported by: alster@vinterdalen.se |
38.92
31 Dec 2024 08:57:55
|
Muhammad Moinur Rahman (bofh) |
Mk/**java.mk: Convert bsd.java.mk to USES
The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
USES=java:build,run if NO_BUILD is undefined. Else it defaults to
USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>
Approved by: mat (portmgr), glewis
Differential Revision: https://reviews.freebsd.org/D48201 |
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) |
38.92
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  ) |
38.92
22 Aug 2021 13:59:58
|
Jason W. Bacon (jwb) |
biology/bbmap: Update to 38.92
Numerous small fixes and enhancements
Reported by: portscout |
38.90
18 Apr 2021 16:21:29
|
Jason W. Bacon (jwb) |
biology/bbmap: BBMap short read aligner, and other bioinformatic tools
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded. |
Number of commits found: 7
|
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