Samtools v0.1.19

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/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. samtools 0.1.19 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds samtools v0.1.19 to your environment"

}

module-whatis "Adds samtools v0.1.19 to your environment"

set samtools_v119_root /cm/shared/apps/SHARED/samtools/samtools-0.1.19:/cm/shared/apps/SHARED/samtools/samtools-0.1.19/bcftools:/cm/shared/apps/SHARED/samtools/samtools-0.1.19/misc

setenv SAMTOOLS_V119 /cm/shared/apps/SHARED/samtools/samtools-0.1.19 prepend-path PATH $samtools_v119_root

</source>

Installation details

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

See also

• Globally installed software
• ABGC specific modules

External links

• Samtools page on Sourceforge