| Port details |
- bwa Burrows-Wheeler sequence aligner
- 0.7.18 biology
 =2      0.7.18Version of this port present on the latest quarterly branch. - Maintainer: alster@vinterdalen.se
- Port Added: 2015-09-25 18:39:48
- Last Update: 2025-01-06 16:29:54
- Commit Hash: b4d1145
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://bio-bwa.sourceforge.net/
- https://sourceforge.net/projects/bio-bwa/
- https://github.com/lh3/bwa/
- Description:
- BWA is a software package for mapping DNA sequences against a large
reference genome, such as the human genome. It consists of three
algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
designed for Illumina sequence reads up to 100bp, while the other two
are for longer sequences ranging from 70bp to a few megabases. BWA-MEM
and BWA-SW share similar features such as the support of long reads
and chimeric alignment, but BWA-MEM, which is the latest, is generally
recommended, as it is faster and more accurate. BWA-MEM also has
better performance than BWA-backtrack for 70-100bp Illumina reads.
For all algorithms, BWA first needs to construct the FM-index for the
reference genome (the "bwa index" command). Alignment algorithms are
invoked with different sub-commands: "bwa aln/samse/sampe" for
BWA-backtrack, "bwa bwasw" for BWA-SW, and "bwa mem" for the BWA-MEM
algorithm.
  ¦  ¦  ¦  ¦ 
- 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/bwa/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/bwa
- pkg install bwa
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: bwa
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1732300398
SHA256 (lh3-bwa-v0.7.18_GH0.tar.gz) = 194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870
SIZE (lh3-bwa-v0.7.18_GH0.tar.gz) = 238036
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:
-
- simde>0 : devel/simde
- gmake>=4.4.1 : devel/gmake
- Runtime dependencies:
-
- perl5>=5.36<5.37 : lang/perl5.36
- This port is required by:
- for Run
-
- biology/atac-seq
- biology/biostar-tools
- biology/chip-seq
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_bwa
- USES:
- gmake localbase perl5 shebangfix
- 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 |
|---|
0.7.18
06 Jan 2025 16:29:54
 |
Zsolt Udvari (uzsolt)
Author: Älven |
biology/bwa: small improvements
Add supplementary WWWs.
Remove unneeded USES=tar:bzip2. Upstream uses common tar.gz archives.
PR: 283873
Approved by: submitter is maintainer |
0.7.18
24 Nov 2024 13:36:38
|
Jason W. Bacon (jwb) |
bwa: New maintainer |
0.7.18
24 Nov 2024 13:31:40
|
Jason W. Bacon (jwb) |
biology/bwa: Update to 0.7.18
Official support for aarch64 (we already had this patched in)
A few minor enhancements and fixes
Changes: https://github.com/lh3/bwa/releases
PR: 282923
Reported by: alster@vinterdalen.se |
0.7.17_2
10 Jan 2024 08:16:01
|
Baptiste Daroussin (bapt) |
MAN?PREFIX: eleminate its usage and move man to share/man |
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) |
0.7.17_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  ) |
0.7.17_1
01 Dec 2021 17:34:18
|
Piotr Kubaj (pkubaj) |
biology/bwa: don't use GCC on powerpc64le
Now that the port uses simde, it builds fine without gcc's translation. |
0.7.17_1
01 Dec 2021 14:56:30
|
Jason W. Bacon (jwb) |
biology/bwa: Unbreak on most non-x86 platforms using simde |
0.7.17
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.7.17
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.7.17
02 Mar 2021 15:01:55
 |
pkubaj |
biology/bwa: fix build on powerpc64le
Use GCC's SSE->Altivec translation:
In file included from ksw.c:29:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion
between vector type '__m64' (vector of 1 'long long' value) and integer type
'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); |
0.7.17
02 Jan 2021 01:46:09
|
linimon |
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.
While here, pet portlint (Makevar order).
Approved by: portmgr (tier-2 blanket) |
0.7.17
28 Aug 2020 11:17:14
|
tcberner |
biology/bwa: fix build on recent current
Obtained
from: https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284 |
0.7.17
31 Jan 2018 01:07:08
|
jwb |
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D14128 |
0.7.17
01 Dec 2017 02:42:54
|
jwb |
[unbreak] biology/bwa: Remove old patch files
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D13314 |
0.7.17
30 Nov 2017 06:13:35
 |
linimon |
For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.
This is part two of a multipart commit to bring armv7 ports to parity
with armv6.
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com -exp run |
0.7.17
28 Nov 2017 15:21:01
|
jwb |
biology/bwa: Upgrade to 0.7.17
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13283 |
0.7.9a
26 May 2017 20:02:44
|
linimon |
Mark some ports failing on armv6, for errors classified as "???".
While here, pet portlint.
Approved by: portmgr (tier-2 blanket) |
0.7.9a
13 May 2017 03:35:51
|
linimon |
Mark some ports failing on power64. In cases where the error message
was a stub, provide a real one.
While here, pet portlint.
Approved by: portmgr (tier-2 blanket) |
0.7.9a
31 Jan 2017 03:40:46
|
linimon |
Mark various ports broken on aarch64 and armv6.
Approved by: portmgr (tier-2 blanket) |
0.7.9a
20 Jan 2017 20:33:31
|
sunpoet |
Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ |
0.7.9a
11 Nov 2016 09:07:21
|
linimon |
Attempt to fix build on non-x86 archs.
Approved by: portmgr (tier-2 blanket) |
0.7.9a
13 Dec 2015 16:07:28
|
swills |
mark some of the ports that don't build on powerpc64 for me |
0.7.9a
11 Dec 2015 08:48:57
|
miwi |
- Update maintainer mail address
- Update/Remove MASTER_SITE
PR: 204755
Submitted by: jwbacon@tds.net (maintainer)
Approved by: mat (mentor)
Differential Revision: D4493 |
0.7.9a
25 Sep 2015 18:39:37
|
rm |
BWA is a program for aligning sequencing reads against a large reference
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon@tds.net> |
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