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Port details on branch 2022Q3
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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: GMAP
WWW:
http://www.gene.com/share/gmap
Description:
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.
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 (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:
TIMESTAMP = 1600434673 SHA256 (gmap-gsnap-2020-09-12.tar.gz) = 9f267d8d165a99b8cb41a22217ed9f8a987ba8b8f8303b0ae867d3e8bf96cef3 SIZE (gmap-gsnap-2020-09-12.tar.gz) = 4470731

Packages (timestamps in pop-ups are UTC):
gmap
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-2020.09.12--2020.09.12---
FreeBSD:13:quarterly-2020.09.12--2020.09.12--2020.09.12
FreeBSD:14:latest-2020.09.12--2020.09.12--2020.09.12
FreeBSD:14:quarterly-2020.09.12--2020.09.12--2020.09.12
FreeBSD:15:latest-2020.09.12n/a-n/a--2020.09.12
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. 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:
===> The following configuration options are available for gmap-2020.09.12: SIMD=off: Use CPU-specific optimizations ===> Use 'make config' to modify these settings
Options name:
biology_gmap
USES:
gmake perl5
pkg-message:
For install:
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:
Expand this list (1 items)
Collapse this list.
  1. http://research-pub.gene.com/gmap/src/
Collapse this list.

There are no commits on branch 2022Q3 for this port