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Port details
gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2015.09.21 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
Maintainer: bacon4000@gmail.com search for ports maintained by this maintainer
Port Added: 29 Sep 2006 04:09:50
License: GMAP
A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.

WWW: http://www.gene.com/share/gmap
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (38 items)
  1. /usr/local/share/licenses/gmap-2015.09.21/catalog.mk
  2. /usr/local/share/licenses/gmap-2015.09.21/LICENSE
  3. /usr/local/share/licenses/gmap-2015.09.21/GMAP
  4. bin/atoiindex
  5. bin/cmetindex
  6. bin/dbsnp_iit
  7. bin/ensembl_genes
  8. bin/fa_coords
  9. bin/get-genome
  10. bin/gff3_genes
  11. bin/gff3_introns
  12. bin/gff3_splicesites
  13. bin/gmap
  14. bin/gmap_build
  15. bin/gmap_compress
  16. bin/gmap_process
  17. bin/gmap_reassemble
  18. bin/gmap_uncompress
  19. bin/gmapindex
  20. bin/gmapl
  21. bin/gsnap
  22. bin/gsnapl
  23. bin/gtf_genes
  24. bin/gtf_introns
  25. bin/gtf_splicesites
  26. bin/gvf_iit
  27. bin/iit_dump
  28. bin/iit_get
  29. bin/iit_store
  30. bin/md_coords
  31. bin/psl_genes
  32. bin/psl_introns
  33. bin/psl_splicesites
  34. bin/sam_sort
  35. bin/snpindex
  36. bin/uniqscan
  37. bin/uniqscanl
  38. bin/vcf_iit
  39. Collapse this list.

To install the port: cd /usr/ports/biology/gmap/ && make install clean
To add the package: pkg install gmap

PKGNAME: gmap

distinfo:

SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake
  2. perl5>=5.24<5.25 : lang/perl5.24
Runtime dependencies:
  1. perl5>=5.24<5.25 : lang/perl5.24
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for gmap-2015.09.21:
     SIMD=off: Use CPU-specific optimizations
===> Use 'make config' to modify these settings

USES:
gmake perl5

pkg-message:
NOTE:

The default configuration for the gmap port disables all optimizations
to maintain compatibility with the widest range of systems.

To get a binary optimized for your system please deinstall gmap and
build from ports using "make config" to enable the SIMD option.

Master Sites:
  1. http://research-pub.gene.com/gmap/src/

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
30 Nov 2017 06:13:35
Original commit files touched by this commit  2015.09.21
Revision:455167  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  2015.09.21
Revision:440746
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  2015.09.21
Revision:434867
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  2015.09.21
Revision:425758
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  2015.09.21
Revision:425675
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  2015.09.21
Revision:403676
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  2015.09.21
Revision:403506
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  2015.09.21
Revision:400336
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  2006.04.21_1
Revision:367328
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  2006.04.21_1
Revision:336070
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  2006.04.21
Revision:327709
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: 15

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