gmap_2019-01-24-1_amd64.deb


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Description

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

Property Value
Distribution Debian 10 (Buster)
Repository Debian Nonfree amd64
Package filename gmap_2019-01-24-1_amd64.deb
Package name gmap
Package version 2019
Package release 01-24-1
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 5.70 MB
Installed size 50.87 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
libbz2-1.0 -
libc6 >= 2.14
perl:any -
zlib1g >= 1:1.2.6

Download

Type URL
Mirror ftp.br.debian.org
Binary Package gmap_2019-01-24-1_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.avx2
/usr/bin/gmap_build
/usr/bin/gmapl
/usr/bin/gmapl.avx2
/usr/bin/gsnap
/usr/bin/gsnap.avx2
/usr/bin/gsnapl
/usr/bin/gsnapl.avx2
/usr/lib/gmap/atoiindex
/usr/lib/gmap/cmetindex
/usr/lib/gmap/cpuid
/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.avx2
/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/gmapl.avx2
/usr/lib/gmap/gsnap
/usr/lib/gmap/gsnap.avx2
/usr/lib/gmap/gsnapl
/usr/lib/gmap/gsnapl.avx2
/usr/lib/gmap/gtf_genes
/usr/lib/gmap/gtf_introns
/usr/lib/gmap/gtf_splicesites
/usr/lib/gmap/gtf_transcript_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/trindex
/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/doc/gmap/examples/tests.tar.xz
/usr/share/lintian/overrides/gmap
/usr/share/man/man1/gmap.1.gz
/usr/share/man/man1/gmap_build.1.gz
/usr/share/man/man1/gsnap.1.gz

Changelog

2019-01-31 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2019-01-24-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* debhelper 12
* Standards-Version: 4.3.0
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
[ Alexandre Mestiashvili ]
* Drop bigendian.patch, as gmap is build for amd64 only
* Set Architecture to amd64 in d/control
* Remove overrides for gmapl* and gsnapl*
2019-01-06 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-07-04-5) unstable; urgency=medium
* Limit architectures to amd64
* Use wildcard for lintian overrides for gmap/gsnap tools
* Upload to unstable
2018-10-04 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-09-27-2) experimental; urgency=medium
* Add patch supposedly fixing builds on MIPS and ARM architectures
2018-09-28 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-09-27-1) experimental; urgency=medium
* New upstream version 2018-09-27
* Set Architecture to any, we want to test if it builds on other archs
* Drop sse2.patch, applied by upstream, refresh install-data-local patch
2018-09-19 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-07-04-4) unstable; urgency=medium
[ Alexandre Mestiashvili ]
* Update d/rules, remove EXTRA_CONFIGURE_ARGS, not needed for recent versions
* Limit architectures to any-amd64 and any-i386
Closes: #908386
2018-08-31 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-07-04-3) unstable; urgency=medium
* Bump Standards-Version to 4.2.1
* Fix a typo in sse2 patch description
* d/control: XS-Autobuild: yes
2018-08-30 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-07-04-2) unstable; urgency=medium
* Add patch from upstream fixing FTBFS when a CPU has only SSE2
2018-07-17 - Alexandre Mestiashvili <mestia@debian.org>
gmap (2018-07-04-1) unstable; urgency=medium
[ Steffen Möller ]
* Updated bio.tools RRID in d/u/metadata
* Update metadata
[ Andreas Tille ]
* Cleanup d/rules
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
[ Alexandre Mestiashvili ]
* Refresh patches
* d/control:
- update Uploader's email
- drop libgmap1{,-dev} as there is no use cases so far
Closes: #903793
* Update d/rules:
- remove --enable-shared as we dropped libgmap1
- add stanza to install tests files to examples
* Remove install files for libgmap1*
* Update d/copyright, remove section for src/saca-k*, update email
* Update lintian-overrides, remove *.nosimd binaries
* Update d/filter.pl to fix gmap man page
* Add autopkgtest
2017-12-21 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
gmap (2017-11-15-1) unstable; urgency=medium
* New upstream version 2017-11-15
* Bump Standards-Version to 4.1.2
2017-11-02 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
gmap (2017-10-30-1) unstable; urgency=medium
* New upstream version 2017-10-30
* Simplify d/rules
* Update symbols file

See Also

Package Description
gmp-doc_6.1.2-1_all.deb GMP (Multiprecision arithmetic library) documentation
grr-client-templates_3.1.0.2-2_all.deb incident response framework - pre-built client templates
gsfonts-other_6.0-4_all.deb Additional fonts for the ghostscript interpreter
gsl-doc-info_2.3-1_all.deb GNU Scientific Library (GSL) Reference Manual in info
gsl-doc-pdf_2.3-1_all.deb GNU Scientific Library (GSL) Reference Manual in pdf
gsl-ref-html_2.3-1_all.deb GNU Scientific Library (GSL) Reference Manual in html
gsl-ref-psdoc_2.3-1_all.deb GNU Scientific Library (GSL) Reference Manual in postscript
hevea-doc_2.32-1_all.deb HeVeA documentation
hijra-applet_0.4.1-1_all.deb Hijri Islamic Calendar tray applet and GNOME shell extension
human-icon-theme_0.28.debian-6.1_all.deb Human Icon theme
hwb_040412-7_all.deb Hardware Book
i965-va-driver-shaders_2.3.0-1_amd64.deb VAAPI driver for Intel G45 & HD Graphics family
icc-profiles_2.1-2_all.deb ICC color profiles for use with color profile aware software
inform-docs_6.31.1+dfsg-2_all.deb documentation for the Inform interactive fiction language (v6)
inform_6.31.1+dfsg-2_amd64.deb story file compiler for the Inform interactive fiction language (v6)
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