Samtools v0.1.12a: Difference between revisions
| Line 3: | Line 3: | ||
== Module file == | == Module file == | ||
The module file can be found in this location: | The module file can be found in this location: | ||
/cm/shared/ | /cm/shared/modulefiles/SHARED/ | ||
<source lang='tcl'> | <source lang='tcl'> | ||
| Line 16: | Line 16: | ||
module-whatis "Adds samtools v0.1.12a to your environment" | module-whatis "Adds samtools v0.1.12a to your environment" | ||
set samtools_v112a_root /cm/shared/apps/ | 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/ | setenv SAMTOOLS_V112a /cm/shared/apps/SHARED/samtools/samtools-0.1.12a | ||
prepend-path PATH $samtools_v112a_root | prepend-path PATH $samtools_v112a_root | ||
</source> | </source> | ||
== Installation details == | == 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. | 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. | ||
Revision as of 10:13, 15 March 2014
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'>
- %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
</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.