View source for Samtools v0.1.12a

[http://samtools.sourceforge.net SAM Tools] provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

== Module file ==
The module file can be found in this location:
  /cm/shared/modulefiles/SHARED/

<pre>
#%Module1.0#######################################################################
## samtools 0.1.12a modulefile
##
proc ModulesHelp { } {

        puts stderr "\tAdds samtools v0.1.12a to your environment"
}

module-whatis   "Adds samtools v0.1.12a to your environment"

set             samtools_v112a_root        /cm/shared/apps/SHARED/samtools/samtools-0.1.12a:/cm/shared/apps/SHARED/samtools/samtools-0.1.12a/bcftools:/cm/shared/apps/SHARED/samtools/samtools-0.1.12a/misc

setenv           SAMTOOLS_V112a   /cm/shared/apps/SHARED/samtools/samtools-0.1.12a
prepend-path     PATH             $samtools_v112a_root

</pre>

== Installation details ==
Compiled from source using gcc 4.8. Note that the module not only prepends the <code>PATH</code> (including path to bcftools), but also sets an additional environment variable <code>SAMTOOLS_V112a</code> which allows mixing various versions of Samtools in a single pipeline if required.

== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

== External links ==
* [http://samtools.sourceforge.net Samtools page on Sourceforge]