Samtools v0.1.19: Difference between revisions

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(Created page with "[http://samtools.sourceforge.net SAM Tools] provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignm...")
 
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== Module file ==
== Module file ==
The module file can be found in this location:
The module file can be found in this location:
   /cm/shared/apps/WUR/ABGC/modulefiles
   /cm/shared/modulefiles/SHARED/


<source lang='tcl'>
<source lang='tcl'>
Line 16: Line 16:
module-whatis  "Adds samtools v0.1.19 to your environment"
module-whatis  "Adds samtools v0.1.19 to your environment"


set            samtools_v119_root        /cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.19:/cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.19/bcftools:/cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.19/misc
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/WUR/ABGC/samtools/samtools-0.1.19
setenv          SAMTOOLS_V119    /cm/shared/apps/SHARED/samtools/samtools-0.1.19
prepend-path    PATH            $samtools_v119_root
prepend-path    PATH            $samtools_v119_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'>

  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

External links