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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 Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: GMAP
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
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
  • scotch
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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
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:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642020.09.122020.09.12
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3862020.09.122020.09.12
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd642020.09.122020.09.12
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3862020.09.122020.09.12
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd642020.09.122020.09.12
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i3862020.09.122020.09.12
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd642020.09.12pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i3862020.09.12pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

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:
WWW: http://www.gene.com/share/gmap
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: 28

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
2020.09.12
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)
2020.09.12
20 Jul 2022 14:20:57
commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2020.09.12
06 Feb 2022 18:36:07
commit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
2020.09.12
10 Jan 2022 15:15:39
commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (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)
2020.09.12
25 Oct 2021 12:58:29
commit hash:61b661339366b6ee95ca1de0667979da9240c6b8commit hash:61b661339366b6ee95ca1de0667979da9240c6b8commit hash:61b661339366b6ee95ca1de0667979da9240c6b8commit hash:61b661339366b6ee95ca1de0667979da9240c6b8 files touched by this commit
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.
2020.09.12
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.
2020.09.12
09 Oct 2020 13:23:13
Revision:551768Original commit files touched by this commit
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.
2020.09.12
22 Sep 2020 00:55:39
Revision:549546Original commit files touched by this commit
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
2015.09.21
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
2015.09.21
21 Jun 2019 11:15:08
Revision:504785Original commit files touched by this commit
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)
2015.09.21
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
2015.09.21
21 Dec 2017 10:23:19
Revision:456901Original commit files touched by this commit
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)
2015.09.21
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
2015.09.21
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)
2015.09.21
26 Feb 2017 12:56:41
Revision:434867Original commit files touched by this commit
linimon search for other commits by this committer
Mark various ports as broken on armv6: invokes x86 asm.

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

Approved by:	portmgr (tier-2 blanket)
2015.09.21
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
2015.09.21
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
2015.09.21
27 Oct 2015 18:49:48
Revision:400336Original commit files touched by this commit
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
2006.04.21_1
05 Sep 2014 09:25:46
Revision:367328Original commit files touched by this commit
antoine search for other commits by this committer
Fix MASTER_SITES

Submitted by:	tijl@
2006.04.21_1
10 Dec 2013 17:21:46
Revision:336070Original commit files touched by this commit
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
2006.04.21
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
2006.04.21
12 Dec 2010 08:10:05
Original commit files touched by this commit
pgollucci search for other commits by this committer
- fix fetch: wget is not required for fetching

Reported by:    QAT
2006.04.21
21 Aug 2008 06:18:49
Original commit files touched by this commit
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)
2006.04.21
16 Apr 2007 21:18:53
Original commit files touched by this commit
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>
2006.04.21
29 Sep 2006 04:05:55
Original commit files touched by this commit
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: 28