Samtools v0.1.12a: Difference between revisions
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(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 == | ||
The module file can be found in this location: | The module file can be found in this location: | ||
/cm/shared/ | /cm/shared/modulefiles/SHARED/ | ||
< | <pre> | ||
#%Module1.0####################################################################### | #%Module1.0####################################################################### | ||
## samtools 0.1.12a modulefile | ## samtools 0.1.12a modulefile | ||
| 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> | </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 == | == See also == | ||
| Line 28: | Line 31: | ||
== External links == | == External links == | ||
* [http:// | * [http://samtools.sourceforge.net Samtools page on Sourceforge] | ||
Latest revision as of 14:51, 15 June 2023
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/
#%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
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.