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Port details
bwa Burrows-Wheeler sequence aligner
0.7.17_1 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 0.7.17Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:39:48
Last Update: 2021-12-01 17:34:18
Commit Hash: f75ac0c
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (7 items)
Collapse this list.
  1. bin/bwa
  2. bin/qualfa2fq.pl
  3. bin/xa2multi.pl
  4. man/man1/bwa.1.gz
  5. /usr/local/share/licenses/bwa-0.7.17_1/catalog.mk
  6. /usr/local/share/licenses/bwa-0.7.17_1/LICENSE
  7. /usr/local/share/licenses/bwa-0.7.17_1/GPLv3
Collapse this list.
Dependency lines:
  • bwa>0:biology/bwa
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
PKGNAME: bwa
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
bwa
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.7.170.7.17
FreeBSD:11:armv6--
FreeBSD:11:i3860.7.170.7.17
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd640.7.17_10.7.17
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.7.17_10.7.17
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd640.7.17_10.7.17
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.7.17_10.7.17
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch640.7.17_1-
FreeBSD:14:amd640.7.17_1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.7.17_1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. simde>0 : devel/simde
  2. gmake>=4.3 : devel/gmake
Runtime dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/ddocent

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/
Collapse this list.

Number of commits found: 19

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
01 Dec 2021 17:34:18
 files touched by this commit commit hash:f75ac0cecdaf833014ca876fb369e788eb342500  0.7.17_1
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bwa: don't use GCC on powerpc64le

Now that the port uses simde, it builds fine without gcc's translation.
01 Dec 2021 14:56:30
 files touched by this commit commit hash:c74d9767d204035f671225a70227a2b24ecb2491  0.7.17_1
Jason W. Bacon (jwb) search for other commits by this committer
biology/bwa: Unbreak on most non-x86 platforms using simde
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  0.7.17
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.7.17
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
02 Mar 2021 15:01:55
Original commit files touched by this commit Revision:566960  0.7.17
pkubaj search for other commits by this committer
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);
02 Jan 2021 01:46:09
Original commit files touched by this commit Revision:559904  0.7.17
linimon search for other commits by this committer
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)
28 Aug 2020 11:17:14
Original commit files touched by this commit Revision:546721  0.7.17
tcberner search for other commits by this committer
biology/bwa: fix build on recent current

Obtained
from:	https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284
31 Jan 2018 01:07:08
Original commit files touched by this commit Revision:460452  0.7.17
jwb search for other commits by this committer
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
01 Dec 2017 02:42:54
Original commit files touched by this commit Revision:455246  0.7.17
jwb search for other commits by this committer
[unbreak] biology/bwa: Remove old patch files

Approved by: jrm
Differential Revision:  https://reviews.freebsd.org/D13314
30 Nov 2017 06:13:35
Original commit files touched by this commit Revision:455167  0.7.17  Sanity Test Failure
linimon search for other commits by this committer
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
28 Nov 2017 15:21:01
Original commit files touched by this commit Revision:455045  0.7.17
jwb search for other commits by this committer
biology/bwa: Upgrade to 0.7.17

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13283
26 May 2017 20:02:44
Original commit files touched by this commit Revision:441814  0.7.9a
linimon search for other commits by this committer
Mark some ports failing on armv6, for errors classified as "???".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
13 May 2017 03:35:51
Original commit files touched by this commit Revision:440746  0.7.9a
linimon search for other commits by this committer
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)
31 Jan 2017 03:40:46
Original commit files touched by this commit Revision:432897  0.7.9a
linimon search for other commits by this committer
Mark various ports broken on aarch64 and armv6.

Approved by:	portmgr (tier-2 blanket)
20 Jan 2017 20:33:31
Original commit files touched by this commit Revision:431996  0.7.9a
sunpoet search for other commits by this committer
Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/
11 Nov 2016 09:07:21
Original commit files touched by this commit Revision:425878  0.7.9a
linimon search for other commits by this committer
Attempt to fix build on non-x86 archs.

Approved by:	portmgr (tier-2 blanket)
13 Dec 2015 16:07:28
Original commit files touched by this commit Revision:403676  0.7.9a
swills search for other commits by this committer
mark some of the ports that don't build on powerpc64 for me
11 Dec 2015 08:48:57
Original commit files touched by this commit Revision:403506  0.7.9a
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
25 Sep 2015 18:39:37
Original commit files touched by this commit Revision:397851  0.7.9a
rm search for other commits by this committer
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>

Number of commits found: 19