Samtools v0.1.12a - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T13:51:23Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 15:51, 15 June 2023
Line 5:		Line 5:
	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## samtools 0.1.12a modulefile		## samtools 0.1.12a modulefile
Line 21:		Line 21:
	prepend-path PATH $samtools_v112a_root		prepend-path PATH $samtools_v112a_root

	</~~source~~>		</pre>

	== Installation details ==		== Installation details ==

Megen002: /* Module file */

2014-03-15T09:13:00Z

Module file

← Older revision		Revision as of 11:13, 15 March 2014
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/~~apps~~/~~WUR~~/~~ABGC/modulefiles~~		/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/~~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		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/~~WUR/ABGC~~/samtools/samtools-0.1.12a		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.

Megen002: /* Installation details */

2013-12-22T19:11:17Z

Installation details

← Older revision		Revision as of 21:11, 22 December 2013
Line 23:		Line 23:
	</source>		</source>
	== Installation details ==		== 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.		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 ==

Megen002 at 19:10, 22 December 2013

2013-12-22T19:10:20Z

← Older revision		Revision as of 21:10, 22 December 2013
Line 1:		Line 1:
	[ 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.		[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 ==

Megen002 at 19:10, 22 December 2013

2013-12-22T19:10:04Z

← Older revision		Revision as of 21:10, 22 December 2013
Line 1:		Line 1:
	[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 for re~~-~~sequencing analysis~~.		[ 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 ==
Line 22:		Line 22:

	</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 ==
Line 28:		Line 30:

	== External links ==		== External links ==
	* [http://~~bio-bwa~~.sourceforge.net~~/bwa.shtml BWA manpage~~]		* [http://samtools.sourceforge.net Samtools page on Sourceforge]

Megen002: 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..."

2013-12-22T19:06:14Z

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..."

New page

[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 for re-sequencing analysis.

== 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>

== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

== External links ==
* [http://bio-bwa.sourceforge.net/bwa.shtml BWA manpage]