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Port details
bwa Burrows-Wheeler sequence aligner
0.7.17_2 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 0.7.17_1Version 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: 2024-01-10 08:16:01
Commit Hash: 1b819e4
License: GPLv3
WWW:
https://sourceforge.net/projects/bio-bwa/
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
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. share/man/man1/bwa.1.gz
  5. /usr/local/share/licenses/bwa-0.7.17_2/catalog.mk
  6. /usr/local/share/licenses/bwa-0.7.17_2/LICENSE
  7. /usr/local/share/licenses/bwa-0.7.17_2/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
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 = 1598613295 SHA256 (lh3-bwa-v0.7.17_GH0.tar.gz) = 980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd SIZE (lh3-bwa-v0.7.17_GH0.tar.gz) = 232593

Expand this list (2 items)

Collapse this list.

SHA256 (2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch) = 15216a79759a2390bda4a4684af34ff3108f63519d2ec3935754507f3c008da0 SIZE (2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch) = 709

Collapse this list.


Packages (timestamps in pop-ups are UTC):
bwa
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.7.17_20.7.17_2-0.7.17_20.7.17_2---
FreeBSD:13:quarterly0.7.17_10.7.17_10.7.17_10.7.17_10.7.17_10.7.17_10.7.17_10.7.17_1
FreeBSD:14:latest0.7.17_20.7.17_20.7.17_10.7.17_20.7.17_20.7.17_1-0.7.17_1
FreeBSD:14:quarterly0.7.17_10.7.17_1-0.7.17_10.7.17_10.7.17_10.7.17_10.7.17_1
FreeBSD:15:latest0.7.17_20.7.17_2n/a0.7.17_2n/a0.7.17_20.7.17_20.7.17_2
FreeBSD:15:quarterly--n/a-n/a---
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>=5.36<5.37 : lang/perl5.36
This port is required by:
for Run
  1. biology/atac-seq
  2. biology/biostar-tools
  3. biology/chip-seq
  4. biology/ddocent

Configuration Options:
No options to configure
Options name:
biology_bwa
USES:
gmake localbase perl5 shebangfix tar:bzip2
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: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.7.17_2
10 Jan 2024 08:16:01
commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070 files touched by this commit
Baptiste Daroussin (bapt) search for other commits by this committer
MAN?PREFIX: eleminate its usage  and move man to share/man
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
0.7.17_1
01 Dec 2021 17:34:18
commit hash: f75ac0cecdaf833014ca876fb369e788eb342500commit hash: f75ac0cecdaf833014ca876fb369e788eb342500commit hash: f75ac0cecdaf833014ca876fb369e788eb342500commit hash: f75ac0cecdaf833014ca876fb369e788eb342500 files touched by this commit
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.
0.7.17_1
01 Dec 2021 14:56:30
commit hash: c74d9767d204035f671225a70227a2b24ecb2491commit hash: c74d9767d204035f671225a70227a2b24ecb2491commit hash: c74d9767d204035f671225a70227a2b24ecb2491commit hash: c74d9767d204035f671225a70227a2b24ecb2491 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bwa: Unbreak on most non-x86 platforms using simde
0.7.17
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.7.17
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.7.17
02 Mar 2021 15:01:55
Revision:566960Original commit files touched by this commit
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);
0.7.17
02 Jan 2021 01:46:09
Revision:559904Original commit files touched by this commit
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)
0.7.17
28 Aug 2020 11:17:14
Revision:546721Original commit files touched by this commit
tcberner search for other commits by this committer
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
Revision:460452Original commit files touched by this commit
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
0.7.17
01 Dec 2017 02:42:54
Revision:455246Original commit files touched by this commit
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
0.7.17
30 Nov 2017 06:13:35
Revision:455167Original commit files touched by this commit 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
0.7.17
28 Nov 2017 15:21:01
Revision:455045Original commit files touched by this commit
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
0.7.9a
26 May 2017 20:02:44
Revision:441814Original commit files touched by this commit
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)
0.7.9a
13 May 2017 03:35:51
Revision:440746Original commit files touched by this commit
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)
0.7.9a
31 Jan 2017 03:40:46
Revision:432897Original commit files touched by this commit
linimon search for other commits by this committer
Mark various ports broken on aarch64 and armv6.

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

Approved by:	portmgr (tier-2 blanket)
0.7.9a
13 Dec 2015 16:07:28
Revision:403676Original commit files touched by this commit
swills search for other commits by this committer
mark some of the ports that don't build on powerpc64 for me
0.7.9a
11 Dec 2015 08:48:57
Revision:403506Original commit files touched by this commit
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
0.7.9a
25 Sep 2015 18:39:37
Revision:397851Original commit files touched by this commit
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: 22