samtools0119-0.1.19-2.3.sdl6.i686.rpm


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Description

samtools0119 - Tools for nucleotide sequence alignments in the SAM format

Property Value
Distribution CentOS 6
Repository PUIAS Computational i386
Package name samtools0119
Package version 0.1.19
Package release 2.3.sdl6
Package architecture i686
Package type rpm
Installed size 1010.26 KB
Download size 437.51 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
samtools0119-0.1.19-2.3.sdl6.x86_64.rpm 0.1.19 x86_64 PUIAS Computational
samtools0119 - - -

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 -
libpthread.so.0 -
libpthread.so.0(GLIBC_2.0) -
libpthread.so.0(GLIBC_2.1) -
libpthread.so.0(GLIBC_2.2) -
libpthread.so.0(GLIBC_2.3.2) -
libtinfo.so.5 -
libz.so.1 -
libz.so.1(ZLIB_1.2.0) -
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
samtools0119 = 0.1.19-2.3.sdl6
samtools0119(x86-32) = 0.1.19-2.3.sdl6

Download

Type URL
Binary Package samtools0119-0.1.19-2.3.sdl6.i686.rpm
Source Package samtools0119-0.1.19-2.3.sdl6.src.rpm

Install Howto

  1. Download 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 samtools0119 rpm package:
    # yum install samtools0119

Files

Path
/usr/local/samtools/0.1.19/bin/bcftools
/usr/local/samtools/0.1.19/bin/blast2sam.pl
/usr/local/samtools/0.1.19/bin/bowtie2sam.pl
/usr/local/samtools/0.1.19/bin/export2sam.pl
/usr/local/samtools/0.1.19/bin/interpolate_sam.pl
/usr/local/samtools/0.1.19/bin/maq2sam-long
/usr/local/samtools/0.1.19/bin/maq2sam-short
/usr/local/samtools/0.1.19/bin/md5fa
/usr/local/samtools/0.1.19/bin/md5sum-lite
/usr/local/samtools/0.1.19/bin/novo2sam.pl
/usr/local/samtools/0.1.19/bin/psl2sam.pl
/usr/local/samtools/0.1.19/bin/razip
/usr/local/samtools/0.1.19/bin/sam2vcf.pl
/usr/local/samtools/0.1.19/bin/samtools
/usr/local/samtools/0.1.19/bin/samtools.pl
/usr/local/samtools/0.1.19/bin/soap2sam.pl
/usr/local/samtools/0.1.19/bin/varfilter.py
/usr/local/samtools/0.1.19/bin/vcfutils.pl
/usr/local/samtools/0.1.19/bin/wgsim
/usr/local/samtools/0.1.19/bin/wgsim_eval.pl
/usr/local/samtools/0.1.19/bin/zoom2sam.pl
/usr/local/samtools/0.1.19/share/man/man1/samtools.1
/usr/share/doc/samtools0119-0.1.19/AUTHORS
/usr/share/doc/samtools0119-0.1.19/COPYING
/usr/share/doc/samtools0119-0.1.19/ChangeLog.old
/usr/share/doc/samtools0119-0.1.19/INSTALL
/usr/share/doc/samtools0119-0.1.19/NEWS
/usr/share/doc/samtools0119-0.1.19/README.bcftools
/usr/share/doc/samtools0119-0.1.19/bcf.tex
/usr/share/doc/samtools0119-0.1.19/examples/00README.txt
/usr/share/doc/samtools0119-0.1.19/examples/Makefile
/usr/share/doc/samtools0119-0.1.19/examples/bam2bed.c
/usr/share/doc/samtools0119-0.1.19/examples/calDepth.c
/usr/share/doc/samtools0119-0.1.19/examples/chk_indel.c
/usr/share/doc/samtools0119-0.1.19/examples/ex1.fa
/usr/share/doc/samtools0119-0.1.19/examples/ex1.sam.gz
/usr/share/doc/samtools0119-0.1.19/examples/toy.fa
/usr/share/doc/samtools0119-0.1.19/examples/toy.sam

Changelog

2013-08-15 - Josko Plazonic <plazonic@math.princeton.edu> - 0.1.19-2
- update to new version
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
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)
scalapack-mpich2-static-1.7.5-10.puias6.i686.rpm Static libraries for ScaLAPACK (mpich2)
scalapack-openmpi-1.7.5-18.sdl6.i686.rpm ScaLAPACK libraries compiled against openmpi
scalapack-openmpi-devel-1.7.5-18.sdl6.i686.rpm Development libraries for ScaLAPACK (openmpi)
scalapack-openmpi-static-1.7.5-18.sdl6.i686.rpm Static libraries for ScaLAPACK (openmpi)
scipy-0.10.1-2.puias6.i686.rpm Scipy: Scientific Tools for Python
scipy27-0.14.1-1.sdl6.i686.rpm Scientific Tools for Python
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