Port details on branch 2022Q3 |
- gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
- 2020.09.12 biology =0 2020.09.12Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- 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.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- Conflicts:
- CONFLICTS_INSTALL:
- 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):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Runtime dependencies:
-
- 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:
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