samtools-0.1.9-3.el5.x86_64.rpm


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Description

samtools - Tools for nucleotide sequence alignments in the SAM format

Property Value
Distribution CentOS 5
Repository PUIAS Computational x86_64
Package name samtools
Package version 0.1.9
Package release 3.el5
Package architecture x86_64
Package type rpm
Installed size 840.81 KB
Download size 403.69 KB
Official Mirror springdale.math.ias.edu
SAM (Sequence Alignment/Map) is a flexible generic format for storing
nucleotide sequence alignment.
SAM Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating
alignments in a per-position format.

Alternatives

Package Version Architecture Repository
samtools-0.1.18-2.el5.i386.rpm 0.1.18 i386 EPEL
samtools-0.1.18-2.el5.x86_64.rpm 0.1.18 x86_64 EPEL
samtools-0.1.9-3.el5.i386.rpm 0.1.9 i386 PUIAS Computational
samtools - - -

Requires

Name Value
/usr/bin/env -
/usr/bin/perl -
/usr/bin/python -
libc.so.6()(64bit) -
libc.so.6(GLIBC_2.2.5)(64bit) -
libc.so.6(GLIBC_2.3)(64bit) -
libc.so.6(GLIBC_2.3.4)(64bit) -
libc.so.6(GLIBC_2.4)(64bit) -
libm.so.6()(64bit) -
libm.so.6(GLIBC_2.2.5)(64bit) -
libncurses.so.5()(64bit) -
libz.so.1()(64bit) -
perl(Carp) -
perl(Data::Dumper) -
perl(File::Spec) -
perl(Getopt::Long) -
perl(Getopt::Std) -
perl(List::Util) -
perl(constant) -
perl(strict) -
perl(warnings) -
rtld(GNU_HASH) -

Provides

Name Value
samtools = 0.1.9-3.el5

Download

Type URL
Binary Package samtools-0.1.9-3.el5.x86_64.rpm
Source Package samtools-0.1.9-3.el5.src.rpm

Install Howto

  1. Create the repository config file /etc/yum.repos.d/puias-computational.repo:
    [puias-computational]
    name=PUIAS Computational
    baseurl=http://springdale.math.ias.edu/data/puias/computational/5/x86_64/
    enabled=1
    gpgcheck=0
    
  2. Install samtools rpm package:
    # yum install samtools

Files

Path
/usr/bin/bcftools
/usr/bin/blast2sam.pl
/usr/bin/bowtie2sam.pl
/usr/bin/export2sam.pl
/usr/bin/interpolate_sam.pl
/usr/bin/maq2sam-long
/usr/bin/maq2sam-short
/usr/bin/md5fa
/usr/bin/md5sum-lite
/usr/bin/novo2sam.pl
/usr/bin/psl2sam.pl
/usr/bin/razip
/usr/bin/sam2vcf.pl
/usr/bin/samtools
/usr/bin/samtools.pl
/usr/bin/soap2sam.pl
/usr/bin/varfilter.py
/usr/bin/varfilter.pyc
/usr/bin/varfilter.pyo
/usr/bin/vcfutils.pl
/usr/bin/wgsim
/usr/bin/wgsim_eval.pl
/usr/bin/zoom2sam.pl
/usr/share/doc/samtools-0.1.9/AUTHORS
/usr/share/doc/samtools-0.1.9/COPYING
/usr/share/doc/samtools-0.1.9/ChangeLog
/usr/share/doc/samtools-0.1.9/INSTALL
/usr/share/doc/samtools-0.1.9/NEWS
/usr/share/doc/samtools-0.1.9/README.bcftools
/usr/share/doc/samtools-0.1.9/bcf.tex
/usr/share/doc/samtools-0.1.9/examples/00README.txt
/usr/share/doc/samtools-0.1.9/examples/Makefile
/usr/share/doc/samtools-0.1.9/examples/bam2bed.c
/usr/share/doc/samtools-0.1.9/examples/calDepth.c
/usr/share/doc/samtools-0.1.9/examples/ex1.fa
/usr/share/doc/samtools-0.1.9/examples/ex1.sam.gz
/usr/share/doc/samtools-0.1.9/examples/toy.fa
/usr/share/doc/samtools-0.1.9/examples/toy.sam
/usr/share/man/man1/samtools.1.gz

Changelog

2013-05-30 - Josko Plazonic <plazonic@math.princeton.edu> - 0.1.9-3
- go back down to 0.1.9 - we need a specific version for this
2011-10-26 - Adam Huffman <verdurin@fedoraproject.org> - 0.1.18-2
- make sure new seqtk tool included
2011-09-06 - Rasmus Ory Nielsen <ron@ron.dk> - 0.1.18-1
- Updated to 0.1.18
2011-05-10 - Rasmus Ory Nielsen <ron@ron.dk> - 0.1.16-1
- Updated to 0.1.16
2011-04-11 - Rasmus Ory Nielsen <ron@ron.dk> - 0.1.15-1
- Updated to 0.1.15
2011-03-23 - Rasmus Ory Nielsen <ron@ron.dk> - 0.1.14-1
- Updated to 0.1.14
- Build shared library instead of static
2011-02-09 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.12a-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
2010-12-06 - Rasmus Ory Nielsen <ron@ron.dk> - 0.1.12a-2
- Fixed header files directory ownership
- Added missing header files
2010-12-06 - Rasmus Ory Nielsen <ron@ron.dk> - 0.1.12a-1
- Updated to 0.1.12a
2010-11-23 - Adam Huffman <bloch@verdurin.com> - 0.1.8-4
- cleanup man page handling

See Also

Package Description
samtools-devel-0.1.9-3.el5.x86_64.rpm Header files and libraries for compiling against samtools
samtools-libs-0.1.9-3.el5.x86_64.rpm Libraries for applications using samtools
samtools0118-0.1.18-2.2.el5.x86_64.rpm Tools for nucleotide sequence alignments in the SAM format
samtools0118-devel-0.1.18-2.2.el5.x86_64.rpm Header files and libraries for compiling against samtools0118
samtools0118-libs-0.1.18-2.2.el5.x86_64.rpm Libraries for applications using samtools0118
samtools0118-pysam26_074-0.7.4-2.el5.x86_64.rpm Python interface for the SAM/BAM sequence alignment and mapping format
samtools0118bv-0.1.18bv-2.2.el5.x86_64.rpm Tools for nucleotide sequence alignments in the SAM format
samtools0118bv-devel-0.1.18bv-2.2.el5.x86_64.rpm Header files and libraries for compiling against samtools0118bv
samtools0118bv-libs-0.1.18bv-2.2.el5.x86_64.rpm Libraries for applications using samtools0118bv
samtools0118bv-pysam26_06-0.6-2.el5.x86_64.rpm Python interface for the SAM/BAM sequence alignment and mapping format
samtools0119-0.1.19-2.2.el5.x86_64.rpm Tools for nucleotide sequence alignments in the SAM format
samtools0119-devel-0.1.19-2.2.el5.x86_64.rpm Header files and libraries for compiling against samtools0119
samtools0119-libs-0.1.19-2.2.el5.x86_64.rpm Libraries for applications using samtools0119
samtools0119-pysam26_075-0.7.5-2.el5.x86_64.rpm Python interface for the SAM/BAM sequence alignment and mapping format
scipy26-0.8.0-4.sdl5.x86_64.rpm Scipy: Scientific Tools for Python
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