Jellyfish 2.1.1 - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T13:49:57Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 15:49, 15 June 2023
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	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## Jellyfish 2.1.1 modulefile		## Jellyfish 2.1.1 modulefile
Line 26:		Line 26:
	prepend-path PKG_CONFIG_PATH $jellyfish_211_pkg		prepend-path PKG_CONFIG_PATH $jellyfish_211_pkg

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

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

Megen002 at 17:59, 15 March 2014

2014-03-15T17:59:36Z

← Older revision		Revision as of 19:59, 15 March 2014
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	~~make -f Makefile.SSE3.gcc~~
	~~make -f Makefile.SSE3.PTHREADS.gcc~~
	~~make -f Makefile.SSE3.MPI.gcc~~

	~~The file <code>Makefile.SSE3.MPI.gcc</code> has been modified:~~
	~~CC = mpicc~~

	~~The version of <code>openmpi</code> used:~~
	~~openmpi/gcc/64/1.6.5~~

	== See also ==		== See also ==

Megen002 at 17:56, 15 March 2014

2014-03-15T17:56:01Z

@@ Line 32: / Line 32: @@
 Compiled from source using the stock gcc 4.4 of Scientific Linux on 15-03-2014:
     http://www.genome.umd.edu/jellyfish.html
 == See also ==

Megen002 at 14:14, 15 March 2014

2014-03-15T14:14:05Z

← Older revision		Revision as of 16:14, 15 March 2014
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	== External links ==		== External links ==
	* [http://~~soap~~.~~genomics~~.~~org~~.cn/~~soapdenovo.html#intro2 SOAPdenovo2~~ home page]		* [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish home page]

Megen002: /* Installation details */

2014-03-15T14:13:33Z

Installation details

← Older revision		Revision as of 16:13, 15 March 2014
Line 32:		Line 32:
	Compiled from source using the stock gcc 4.4 of Scientific Linux on 15-03-2014:		Compiled from source using the stock gcc 4.4 of Scientific Linux on 15-03-2014:
	http://www.genome.umd.edu/jellyfish.html		http://www.genome.umd.edu/jellyfish.html
	~~This included the GapCloser software (v1.12), ErrorCorrection (v0.04), and SOAPec (v2.01, includes Corrector_AR, Corrector_HA, KmerFreq_AR and KmerFreq_HA binaries).~~

	== See also ==		== See also ==

Megen002 at 14:13, 15 March 2014

2014-03-15T14:13:16Z

← Older revision		Revision as of 16:13, 15 March 2014
Line 1:		Line 1:
	'''[http://~~soap~~.~~genomics~~.~~org~~.cn/~~soapdenovo.html#intro2 SOAPdenovo2~~]''' is a ~~popular genome assembler~~.		'''[http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish]''' is a fast, parallel k-mer counter for DNA.


	== Module file ==		== Module file ==

Megen002: /* Installation details */

2014-03-15T14:12:38Z

Installation details

← Older revision		Revision as of 16:12, 15 March 2014
Line 31:		Line 31:
	== Installation details ==		== Installation details ==

	~~The pre-compiled binaries were downloaded~~ from ~~SourceForge~~ on 15-03-2014:		Compiled from source using the stock gcc 4.4 of Scientific Linux on 15-03-2014:
	http://~~sourceforge~~.~~net/projects/soapdenovo2/files/SOAPdenovo2~~/		http://www.genome.umd.edu/jellyfish.html
	This included the GapCloser software (v1.12), ErrorCorrection (v0.04), and SOAPec (v2.01, includes Corrector_AR, Corrector_HA, KmerFreq_AR and KmerFreq_HA binaries).		This included the GapCloser software (v1.12), ErrorCorrection (v0.04), and SOAPec (v2.01, includes Corrector_AR, Corrector_HA, KmerFreq_AR and KmerFreq_HA binaries).

Megen002: Created page with "'''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/..."

2014-03-15T14:10:21Z

Created page with "'''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/..."

New page

'''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler.

== Module file ==
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/

<source lang='tcl'>
#%Module1.0#######################################################################
## Jellyfish 2.1.1 modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds Jellyfish 2.1.1 to your environment"
}

module-whatis "Adds Jellyfish 2.1.1 to your environment"

set jellyfish_211_bin /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/bin
set jellyfish_211_ldpath /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/lib
set jellyfish_211_man /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/share/man
set jellyfish_211_pkg /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/lib/pkgconfig

prepend-path PATH $jellyfish_211_bin
prepend-path LD_LIBRARY_PATH $jellyfish_211_ldpath
prepend-path MANPATH $jellyfish_211_man
prepend-path PKG_CONFIG_PATH $jellyfish_211_pkg

</source>

== Installation details ==

The pre-compiled binaries were downloaded from SourceForge on 15-03-2014:
http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/
This included the GapCloser software (v1.12), ErrorCorrection (v0.04), and SOAPec (v2.01, includes Corrector_AR, Corrector_HA, KmerFreq_AR and KmerFreq_HA binaries).

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

== External links ==
* [http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2 home page]