Samtools v0.1.12a: Difference between revisions
(Created page with "[http://en.wikipedia.org/wiki/Burrows-Wheeler_Aligner#Short-Read_Sequence_Alignment BWA] is a short read aligner designed by Heng Li and currently the most widely used aligner...") |
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[http:// | [ 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 == | == Module file == | ||
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</source> | </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 == | == See also == | ||
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== External links == | == External links == | ||
* [http:// | * [http://samtools.sourceforge.net Samtools page on Sourceforge] | ||
Revision as of 20:10, 22 December 2013
[ 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/apps/WUR/ABGC/modulefiles
<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/WUR/ABGC/samtools/samtools-0.1.12a:/cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.12a/bcftools:/cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.12a/misc
setenv SAMTOOLS_V112a /cm/shared/apps/WUR/ABGC/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.