gmap_2014-10-22-1_amd64.deb


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Description

gmap - spliced and SNP-tolerant alignment for mRNA and short reads

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Nonfree amd64
Package filename gmap_2014-10-22-1_amd64.deb
Package name gmap
Package version 2014
Package release 10-22-1
Package architecture amd64
Package type deb
Category field::biology field::biology:bioinformatics field::biology:structural non-free/science role::program use::analysing
Homepage http://research-pub.gene.com/gmap
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 8.96 MB
Installed size 72.21 MB
This package contains the programs GMAP and GSNAP as well as
utilities to manage genome databases in GMAP/GSNAP format.
GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
EST, mRNA and cDNA sequences.
GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
aligning single-end and paired-end transcriptome reads.
Both tools can use a database of
* known splice sites and identify novel splice sites.
* known single-nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.

Alternatives

Package Version Architecture Repository
gmap - - -

Requires

Name Value
libc6 >= 2.14
perl -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package gmap_2014-10-22-1_amd64.deb
Source Package gmap

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install gmap deb package:
    # sudo apt-get install gmap

Files

Path
/usr/bin/gmap
/usr/bin/gmap_build
/usr/bin/gsnap
/usr/lib/gmap/atoiindex
/usr/lib/gmap/cmetindex
/usr/lib/gmap/dbsnp_iit
/usr/lib/gmap/ensembl_genes
/usr/lib/gmap/fa_coords
/usr/lib/gmap/get-genome
/usr/lib/gmap/gff3_genes
/usr/lib/gmap/gff3_introns
/usr/lib/gmap/gff3_splicesites
/usr/lib/gmap/gmap
/usr/lib/gmap/gmap_build
/usr/lib/gmap/gmap_compress
/usr/lib/gmap/gmap_process
/usr/lib/gmap/gmap_reassemble
/usr/lib/gmap/gmap_uncompress
/usr/lib/gmap/gmapindex
/usr/lib/gmap/gmapl
/usr/lib/gmap/gsnap
/usr/lib/gmap/gsnapl
/usr/lib/gmap/gtf_genes
/usr/lib/gmap/gtf_introns
/usr/lib/gmap/gtf_splicesites
/usr/lib/gmap/gvf_iit
/usr/lib/gmap/iit_dump
/usr/lib/gmap/iit_get
/usr/lib/gmap/iit_store
/usr/lib/gmap/md_coords
/usr/lib/gmap/psl_genes
/usr/lib/gmap/psl_introns
/usr/lib/gmap/psl_splicesites
/usr/lib/gmap/sam_sort
/usr/lib/gmap/snpindex
/usr/lib/gmap/uniqscan
/usr/lib/gmap/uniqscanl
/usr/lib/gmap/vcf_iit
/usr/share/doc/gmap/AUTHORS
/usr/share/doc/gmap/NOTICE.gz
/usr/share/doc/gmap/README.Debian
/usr/share/doc/gmap/README.gz
/usr/share/doc/gmap/changelog.Debian.gz
/usr/share/doc/gmap/changelog.gz
/usr/share/doc/gmap/copyright
/usr/share/man/man1/gmap.1.gz
/usr/share/man/man1/gmap_build.1.gz
/usr/share/man/man1/gsnap.1.gz

Changelog

2014-10-26 - Andreas Tille <tille@debian.org>
gmap (2014-10-22-1) unstable; urgency=medium
[ Alexandre Mestiashvili ]
* build fails due to 2 failing test on i386 for 2014-10-14
[ Andreas Tille ]
* Imported Upstream version 2014-10-22
[ Alexandre Mestiashvili ]
* debian/*.1: updated dates in man pages
* d/patches/drop_tests_i386.patch: do not run tests on i386 because they fail.
As it is not clear if the program is useful on i386 architecure, 
let's leave it like that for now.
* d/README.Debian: note that embeded tests are skipped for i386
2014-10-11 - Andreas Tille <tille@debian.org>
gmap (2014-10-09-1) unstable; urgency=medium
* New upstream version
* cme fix dpkg-control
* DEP5 fix
2014-07-30 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
gmap (2014-07-28-1) unstable; urgency=medium
* Imported Upstream version 2014-07-28
2014-07-04 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
gmap (2014-07-04-1) unstable; urgency=medium
* New upstream release
2014-07-04 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
gmap (2014-06-10-1) UNRELEASED; urgency=medium
* New upstream release
* debian/patches/install-data-local: refreshed
* d/control: use canonical Vcs fields 
- updated Standards-Version   
- added help2man to Build-Depends:   
- remove trailing slash from Homepage  
- added myself to Uploaders:
* d/rules: install symlinks for gmap,gsnap and gmap_build in /usr/bin   
- use as bindir /usr/lib/gmap   
* d/install: removed as all files are installed in /usr/lib/gmap
* d/copyright:
- refresh copyright, add not mentioned before files
- add Comment that code was influenced by another software
* debian/*.1:  updated man pages  
* d/docs: install NOTICE
2013-08-02 - Andreas Tille <tille@debian.org>
gmap (2013-07-20-1) unstable; urgency=low
* New upstream version
* debian/control:
- cme fix dpkg-control
- debhelper 9
2012-06-12 - Shaun Jackman <sjackman@debian.org>
gmap (2012-06-12-1) unstable; urgency=low
* New upstream release
2012-04-01 - Andreas Tille <tille@debian.org>
gmap (2012-03-23-1) UNRELEASED; urgency=low
* New upstream release
* debian/control:
- Added myself to Uploaders
- Standards-Version: 3.9.3 (no changes needed)
* debhelper 8 (control+compat)
* debian/upstream: Add citation information
* debian/copyright: Fixed some DEP5 issues and verified using
cme fix dpkg-copyright
* debian/install: gsnap_tally is not builded any more in this version
* debian/rules: really use autotools-dev to enable building twice in
a row
2011-12-29 - Shaun Jackman <sjackman@debian.org>
gmap (2011-12-28-1) unstable; urgency=low
* New upstream release.
2011-12-07 - Shaun Jackman <sjackman@debian.org>
gmap (2011-11-30-1) unstable; urgency=low
* New upstream release.

See Also

Package Description
gmp-doc_6.0.0-1_all.deb GMP (Multiprecision arithmetic library) documentation
gnat-4.8-doc_4.8.3-1_all.deb documentation for the GNU Ada Compiler (gnat)
gnat-4.9-doc_4.9.1-3_all.deb documentation for the GNU Ada Compiler (gnat)
gsfonts-other_6.0-4_all.deb Additional fonts for the ghostscript interpreter
gsl-doc-info_1.16-1_all.deb GNU Scientific Library (GSL) Reference Manual in info
gsl-doc-pdf_1.16-1_all.deb GNU Scientific Library (GSL) Reference Manual in pdf
gsl-ref-html_1.16-1_all.deb GNU Scientific Library (GSL) Reference Manual in html
gsl-ref-psdoc_1.16-1_all.deb GNU Scientific Library (GSL) Reference Manual in postscript
hevea-doc_2.18-1_all.deb HeVeA documentation
hijra-applet_0.2.1-1_all.deb Hijri Islamic Calendar tray applet and GNOME shell extension
human-icon-theme_0.28.debian-3.4~deb8u1_all.deb Human Icon theme
hwb_040412-6_all.deb Hardware Book
icc-profiles_2.0.1-1_all.deb ICC color profiles for use with color profile aware software
igv_2.3.38+dfsg-1_all.deb Integrative Genomics Viewer
inform-docs_6.31.1+dfsg-1.1_all.deb documentation for the Inform interactive fiction language (v6)
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