samtools-0.1.9-4.sdl6.i686.rpm


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Description

samtools - Tools for nucleotide sequence alignments in the SAM format

Property Value
Distribution CentOS 6
Repository PUIAS Computational i386
Package name samtools
Package version 0.1.9
Package release 4.sdl6
Package architecture i686
Package type rpm
Installed size 856.44 KB
Download size 367.09 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.el6.i686.rpm 0.1.18 i686 EPEL
samtools-0.1.18-2.el6.x86_64.rpm 0.1.18 x86_64 EPEL
samtools-0.1.9-4.sdl6.x86_64.rpm 0.1.9 x86_64 PUIAS Computational
samtools - - -

Requires

Name Value
/usr/bin/env -
/usr/bin/perl -
/usr/bin/python -
libc.so.6(GLIBC_2.7) -
libm.so.6 -
libm.so.6(GLIBC_2.0) -
libncurses.so.5 -
libtinfo.so.5 -
libz.so.1 -
libz.so.1(ZLIB_1.2.2) -
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 = 0.1.9-4.sdl6
samtools(x86-32) = 0.1.9-4.sdl6

Download

Type URL
Binary Package samtools-0.1.9-4.sdl6.i686.rpm
Source Package samtools-0.1.9-4.sdl6.src.rpm

Install Howto

  1. Download the latest puias-computational rpm from
    http://springdale.math.ias.edu/data/puias/computational/6/i386/
  2. Install puias-computational rpm:
    # rpm -Uvh puias-computational*rpm
  3. 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/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-0.1.9-4.sdl6.i686.rpm Header files and libraries for compiling against samtools
samtools-libs-0.1.9-4.sdl6.i686.rpm Libraries for applications using samtools
samtools0118-0.1.18-2.3.sdl6.i686.rpm Tools for nucleotide sequence alignments in the SAM format
samtools0118-devel-0.1.18-2.3.sdl6.i686.rpm Header files and libraries for compiling against samtools0118
samtools0118-libs-0.1.18-2.3.sdl6.i686.rpm Libraries for applications using samtools0118
samtools0119-0.1.19-2.3.sdl6.i686.rpm Tools for nucleotide sequence alignments in the SAM format
samtools0119-devel-0.1.19-2.3.sdl6.i686.rpm Header files and libraries for compiling against samtools0119
samtools0119-libs-0.1.19-2.3.sdl6.i686.rpm Libraries for applications using samtools0119
samtools0119-pysam27_075-0.7.5-2.1.sdl6.i686.rpm Python interface for the SAM/BAM sequence alignment and mapping format
scalapack-common-1.7.5-18.sdl6.i686.rpm Common files for scalapack
scalapack-mpich-1.7.5-18.sdl6.i686.rpm ScaLAPACK libraries compiled against mpich
scalapack-mpich-devel-1.7.5-18.sdl6.i686.rpm Development libraries for ScaLAPACK (mpich)
scalapack-mpich-static-1.7.5-18.sdl6.i686.rpm Static libraries for ScaLAPACK (mpich)
scalapack-mpich2-1.7.5-10.puias6.i686.rpm ScaLAPACK libraries compiled against mpich2
scalapack-mpich2-devel-1.7.5-10.puias6.i686.rpm Development libraries for ScaLAPACK (mpich2)
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