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Port details
gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2020.09.12 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 2020.09.12Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-09-29 04:09:50
Last Update: 2022-01-10 15:15:39
Commit Hash: bcaf25a
License: GMAP
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (45 items)
Collapse this list.
  1. /usr/local/share/licenses/gmap-2020.09.12/catalog.mk
  2. /usr/local/share/licenses/gmap-2020.09.12/LICENSE
  3. /usr/local/share/licenses/gmap-2020.09.12/GMAP
  4. bin/atoiindex
  5. bin/cmetindex
  6. bin/cpuid
  7. bin/dbsnp_iit
  8. bin/ensembl_genes
  9. bin/fa_coords
  10. bin/get-genome
  11. bin/gff3_genes
  12. bin/gff3_introns
  13. bin/gff3_splicesites
  14. bin/gmap
  15. bin/gmap.nosimd
  16. bin/gmap_build
  17. bin/gmap_cat
  18. bin/gmap_process
  19. bin/gmapindex
  20. bin/gmapl
  21. bin/gmapl.nosimd
  22. bin/gsnap
  23. bin/gsnap.nosimd
  24. bin/gsnapl
  25. bin/gsnapl.nosimd
  26. bin/gtf_genes
  27. bin/gtf_introns
  28. bin/gtf_splicesites
  29. bin/gtf_transcript_splicesites
  30. bin/gvf_iit
  31. bin/iit_dump
  32. bin/iit_get
  33. bin/iit_store
  34. bin/indexdb_cat
  35. bin/md_coords
  36. bin/psl_genes
  37. bin/psl_introns
  38. bin/psl_splicesites
  39. bin/sam_sort
  40. bin/snpindex
  41. bin/trindex
  42. bin/vcf_iit
  43. @owner
  44. @group
  45. @mode
Collapse this list.
Dependency lines:
  • gmap>0:biology/gmap
Conflicts:
CONFLICTS_INSTALL:
  • cpuid
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/gmap/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/gmap
  • pkg install gmap
PKGNAME: gmap
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64 i386 powerpc64le
distinfo:
Packages (timestamps in pop-ups are UTC):
gmap
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642020.09.122020.09.12
FreeBSD:11:armv6--
FreeBSD:11:i3862020.09.122020.09.12
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642020.09.122020.09.12
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3862020.09.122020.09.12
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd642020.09.122020.09.12
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3862020.09.122020.09.12
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd642020.09.12-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862020.09.12-
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. gmake>=4.3 : devel/gmake
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

pkg-message:
For install:
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://research-pub.gene.com/gmap/src/
Collapse this list.

Number of commits found: 24

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Jan 2022 15:15:39
 files touched by this commit commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1  2020.09.12
Stefan E├čer (se) search for other commits by this committer
Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above View all of this commit message)
25 Oct 2021 12:58:29
 files touched by this commit commit hash:61b661339366b6ee95ca1de0667979da9240c6b8  2020.09.12
Alexey Dokuchaev (danfe) search for other commits by this committer
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)

ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.

While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2020.09.12
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
09 Oct 2020 13:23:13
Original commit files touched by this commit Revision:551768  2020.09.12
pkubaj search for other commits by this committer
biology/gmap: enable on powerpc64le

Doesn't build on powerpc64 due to missing big-endian code variants, but builds
on powerpc64le.
22 Sep 2020 00:55:39
Original commit files touched by this commit Revision:549546  2020.09.12
jwb search for other commits by this committer
biology/gmap: Upgrade to 2020.09.12

First upgrade in 5 years, so numerous improvements
Unsure if powerpc is still supported upstream
Code mentions power8, but does not build on my Mac G5
13 Aug 2019 16:00:39
Original commit files touched by this commit Revision:508834  2015.09.21
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
21 Jun 2019 11:15:08
Original commit files touched by this commit Revision:504785  2015.09.21
linimon search for other commits by this committer
Enable workaround for building on powerpc64.

Autoconf reports that HAVE_ASM_BSR is true (1).  However, it's a false
positive.

I do not have enough knowledge of autoconf to fix this problem correctly,
so fix src/config.h in post-configure.  Patches welcome.

A proper fix will most likely also fix the build on other tier-2 archs,
but I have not taken the time to test that yet.

Approved by:	portmgr (tier-2 blanket)
31 Jan 2018 01:07:08
Original commit files touched by this commit Revision:460452  2015.09.21
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
21 Dec 2017 10:23:19
Original commit files touched by this commit Revision:456901  2015.09.21
linimon search for other commits by this committer
Try to bring some consistency to ports that have x86-specific pieces.

 - in general, if we think that the code is not architecture-specific,
   and instead just enables x86 assembler by default, those should
   use BROKEN rather than IGNORE.  This will allow them to be attempted
   with TRYBROKEN.
 - spell i386 as x86.
 - spell asm as assembler.
 - pet portlint.

These changes should have no effect on tier-1 builds.

Approved by:	portmgr (tier-2 blanket)
30 Nov 2017 06:13:35
Original commit files touched by this commit Revision:455167  2015.09.21  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
13 May 2017 03:35:51
Original commit files touched by this commit Revision:440746  2015.09.21
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)
26 Feb 2017 12:56:41
Original commit files touched by this commit Revision:434867  2015.09.21
linimon search for other commits by this committer
Mark various ports as broken on armv6: invokes x86 asm.

Approved by:	portmgr (tier-2 blanket)
08 Nov 2016 19:29:57
Original commit files touched by this commit Revision:425758  2015.09.21
linimon search for other commits by this committer
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
08 Nov 2016 03:40:15
Original commit files touched by this commit Revision:425675  2015.09.21
linimon search for other commits by this committer
Mark broken on all tier-2 archs.

Approved by:	portmgr (tier-2 blanket)
13 Dec 2015 16:07:28
Original commit files touched by this commit Revision:403676  2015.09.21
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  2015.09.21
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
27 Oct 2015 18:49:48
Original commit files touched by this commit Revision:400336  2015.09.21
madpilot search for other commits by this committer
- Update to 2015.09.21
- Add License
- Add SIMD option disabled by default to avoid creating official
  packags with CPU specific optimizations
- Add pkg-message explaining how to get an optimized binary
- Assign maintainership to submitter

PR:		203334
Submitted by:	jwbacon at tds.net
Approved by:	Maintainer timeout
05 Sep 2014 09:25:46
Original commit files touched by this commit Revision:367328  2006.04.21_1
antoine search for other commits by this committer
Fix MASTER_SITES

Submitted by:	tijl@
10 Dec 2013 17:21:46
Original commit files touched by this commit Revision:336070  2006.04.21_1
bapt search for other commits by this committer
Support stage
Convert USE_GMAKE to USES=gmake
Add dependency on perl which the port need and was getting by chance
bump portrevision, dependencies has changed
20 Sep 2013 15:55:44
Original commit files touched by this commit Revision:327709  2006.04.21
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
12 Dec 2010 08:10:05
Original commit files touched by this commit   2006.04.21
pgollucci search for other commits by this committer
- fix fetch: wget is not required for fetching

Reported by:    QAT
21 Aug 2008 06:18:49
Original commit files touched by this commit   2006.04.21
rafan search for other commits by this committer
Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk
(Only the first 15 lines of the commit message are shown above View all of this commit message)
16 Apr 2007 21:18:53
Original commit files touched by this commit   2006.04.21
edwin search for other commits by this committer
[patch] cleanup non-supported FreeBSD versions

PR:             ports/111727
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    Bob Zimmermann <rpz@cse.wustl.edu>
29 Sep 2006 04:05:55
Original commit files touched by this commit   2006.04.21
clsung search for other commits by this committer
Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA
and EST Sequences.

PR:             ports/103651
Submitted by:   Bob Zimmermann <rpz at cse.wustl.edu>

Number of commits found: 24