cufflinks_2.2.1-1+b1_amd64.deb


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Description

cufflinks - Transcript assembly, differential expression and regulation for RNA-Seq

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Nonfree amd64
Package filename cufflinks_2.2.1-1+b1_amd64.deb
Package name cufflinks
Package version 2.2.1
Package release 1+b1
Package architecture amd64
Package type deb
Category non-free/science
Homepage http://cufflinks.cbcb.umd.edu
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 1.39 MB
Installed size 9.67 MB
Cufflinks assembles transcripts, estimates their abundances, and tests for
differential expression and regulation in RNA-Seq samples. It accepts aligned
RNA-Seq reads and assembles the alignments into a parsimonious set of
transcripts. Cufflinks then estimates the relative abundances of these
transcripts based on how many reads support each one.

Alternatives

Package Version Architecture Repository
cufflinks - - -

Requires

Name Value
libboost-serialization1.55.0 -
libboost-system1.55.0 -
libboost-thread1.55.0 -
libc6 >= 2.14
libgcc1 >= 1:4.1.1
libstdc++6 >= 4.9
python -
zlib1g >= 1:1.2.3.3

Download

Type URL
Mirror ftp.br.debian.org
Binary Package cufflinks_2.2.1-1+b1_amd64.deb
Source Package cufflinks

Install Howto

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

Files

Path
/usr/bin/compress_gtf
/usr/bin/cuffcompare
/usr/bin/cuffdiff
/usr/bin/cufflinks
/usr/bin/cuffmerge
/usr/bin/cuffnorm
/usr/bin/cuffquant
/usr/bin/gffread
/usr/bin/gtf_to_sam
/usr/share/doc/cufflinks/AUTHORS
/usr/share/doc/cufflinks/README
/usr/share/doc/cufflinks/changelog.Debian.amd64.gz
/usr/share/doc/cufflinks/changelog.Debian.gz
/usr/share/doc/cufflinks/copyright
/usr/share/man/man1/compress_gtf.1.gz
/usr/share/man/man1/cuffcompare.1.gz
/usr/share/man/man1/cuffdiff.1.gz
/usr/share/man/man1/cufflinks.1.gz
/usr/share/man/man1/cuffmerge.1.gz
/usr/share/man/man1/cuffnorm.1.gz
/usr/share/man/man1/cuffquant.1.gz
/usr/share/man/man1/gffread.1.gz
/usr/share/man/man1/gtf_to_sam.1.gz

Changelog

2014-05-16 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
cufflinks (2.2.1-1) unstable; urgency=medium
* d/control: cme fix dpkg-control
* Imported Upstream version 2.2.1
2014-04-11 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
cufflinks (2.2.0-1) unstable; urgency=medium
[ James McCoy ]
* Move debian/upstream to debian/upstream/metadata
[ Alexandre Mestiashvili ]
* Imported Upstream version 2.2.0
* d/rules: 
- link to the serialization library "-lboost_serialization"
- generate man pages automatically with help2man 
- separate rule for manpage for gffread as it doesn't return usage
message when executed without arguments  
* d/control: 
- use canonical VCS-* fields
- updated Standards-Version
- Build-Depends: add help2man
* d/patches/gffread_show_usage.patch: fix wrong USAGE indentation causing
buffer overflow in gffread when using -h, --help and some other arguments
* d/*.1: removed obsoleted manpages
* d/copyright: updated Source, Copyright years
2013-10-23 - Dmitrijs Ledkovs <xnox@ubuntu.com>
cufflinks (2.1.1-4) unstable; urgency=low
* Force use boost_system, boost_thread when linking. Fixing FTBFS in
ubuntu.
* Enable parallel build.
2013-09-07 - Dmitrijs Ledkovs <xnox@debian.org>
cufflinks (2.1.1-3) unstable; urgency=low
* Rebuild against boost1.54.
2013-05-23 - Dmitrijs Ledkovs <xnox@debian.org>
cufflinks (2.1.1-2) unstable; urgency=low
* Fix failing to build from source against boost1.53. (Closes: #709252)
2013-05-22 - Andreas Tille <tille@debian.org>
cufflinks (2.1.1-1) unstable; urgency=low
[Carlos Borroto]
* New upstream release.
* Added libeigen3-dev to build-deps.
* Modified fix_includes_path to properly include Eigen library.
* Bumped libboost-dev requirement to >= 1.47.0
[ Alexandre Mestiashvili ]
* Imported debian/patches/0004-fix-m64-usage-and-lfs.patch, Closes: #675985
[ Andreas Tille ]
* Upstream release 2.1.1 (+ adapted patches)
Closes: #687968
* debian/control:
- Removed: DM-Upload-Allowed
- Standards-Version: 3.9.4
- Debhelper 9 (also d/compat)
requires d/p/format-security.patch for hardening via --format-security
- normalised format
2012-05-24 - Charles Plessy <plessy@debian.org>
cufflinks (1.3.0-2) unstable; urgency=low
[ Charles Plessy ]
* Normalised and summarised debian/copyright.
[ Carlos Borroto ]
* Added tophat to Enhances
[ Andreas Tille ]
* debian/upstream: Added references as specified in tasks file
* debian/copyright: Added Upstream-Contact e-mail
* debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue
Closes: #672744
2012-01-06 - Charles Plessy <plessy@debian.org>
cufflinks (1.3.0-1) unstable; urgency=low
[ Alexandre Mestiashvili ]
* New upstream release
* Fixed spelling error.
* Updated source version
[ Charles Plessy ]
* Removed quilt patch management, and rely on dpkg-dev exclusively.
2011-12-11 - Charles Plessy <plessy@debian.org>
cufflinks (1.2.1-1) unstable; urgency=low
[ Alexandre Mestiashvili ]
* New upstream release
* added patch to fix bam.h location .
* debian/rules invoke autoreconf
* debian/rules added overrides for dh_auto_clean and dh_clean
* added missing dependency - quilt .We use dh_quilt_patch,
dh_quilt_unpatch helpers
* debian/control added dependency python (>=2.6.6-3~) for source package
* debian/control added dependency python (>=2.6.6-3~) for binary package
[ Andreas Tille ]
* Added myself to uploaders
* Debhelper 8 (control+compat)
* debian/watch: removed dh-make template from watch file
* debian/rules: invoke autotools_dev
[ Charles Plessy ]
* Switch to non-free section because of the locfit license (debian/control).
* Added myself to Uploaders (debian/control).
* Compress binary package with xz (debian/rules).
* Pre-depend on dpkg (>= 1.15.6) for xz compression (Ubuntu LTS).

See Also

Package Description
cuneiform-common_1.1.0+dfsg-5_all.deb multi-language OCR system (common)
cuneiform_1.1.0+dfsg-5_amd64.deb multi-language OCR system
d1x-rebirth_0.58.1-1_amd64.deb port of the 1995 classic game Descent 1: First Strike
d2x-rebirth_0.58.1-1_amd64.deb port of the 1996 classic game Descent 2: Counterstrike
dahdi-firmware-nonfree_2.10.0-1_all.deb DAHDI non-free firmware
distributed-net_2.9111.520-2_amd64.deb client to donate unused CPU cycles to distributed.net
doc-rfc-experimental_20120225-2_all.deb Experimental RFCs
doc-rfc-fyi-bcp_20120225-2_all.deb FYI and BCP RFCs
doc-rfc-informational_20120225-2_all.deb Informational RFCs
doc-rfc-misc_20120225-2_all.deb Historic and draft RFCs
doc-rfc-old-std_20120225-2_all.deb Old Standard RFCs
doc-rfc-others_20120225-2_all.deb Old experimental and unclassified RFCs
doc-rfc-std-proposed_20120225-2_all.deb Proposed Standard RFCs
doc-rfc-std_20120225-2_all.deb Standard RFCs
doc-rfc_20120225-2_all.deb RFC documents metapackage
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