Allpathslg 51910 - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T14:41:36Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 16:41, 15 June 2023
Line 7:		Line 7:
	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## maker ALLPATHS-LG (51910 modulefile		## maker ALLPATHS-LG (51910 modulefile
Line 26:		Line 26:


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

	== Installation details ==		== Installation details ==
Line 32:		Line 32:
	ALLPATHS-LG 51910 was downloades as 'latest version':		ALLPATHS-LG 51910 was downloades as 'latest version':

	<~~source lang='bash'~~>		<pre>
	wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz		wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz
	</~~source~~>		</pre>

	It was compiled from source (using gcc4.8.1) on 03-02-2015:		It was compiled from source (using gcc4.8.1) on 03-02-2015:

	<~~source lang='bash'~~>		<pre>
	module load gcc/4.8.1		module load gcc/4.8.1
	./configure --prefix=/cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910		./configure --prefix=/cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910
	make		make
	make install		make install
	</~~source~~>		</pre>

	Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly.		Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly.
	Testgenome derived from here and instructions followed in README:		Testgenome derived from here and instructions followed in README:

	<~~source lang='bash'~~>		<pre>
	wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz		wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz
	</~~source~~>		</pre>

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

Megen002 at 15:42, 4 February 2015

2015-02-04T15:42:32Z

← Older revision		Revision as of 17:42, 4 February 2015
Line 46:		Line 46:

	Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly.		Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly.
			Testgenome derived from here and instructions followed in README:

			<source lang='bash'>
			wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz
			</source>

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

Megen002 at 13:51, 4 February 2015

2015-02-04T13:51:44Z

← Older revision		Revision as of 15:51, 4 February 2015
Line 45:		Line 45:
	</source>		</source>

	Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment.		Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly.

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

Megen002 at 13:50, 4 February 2015

2015-02-04T13:50:11Z

← Older revision		Revision as of 15:50, 4 February 2015
Line 31:		Line 31:

	ALLPATHS-LG 51910 was downloades as 'latest version':		ALLPATHS-LG 51910 was downloades as 'latest version':

			<source lang='bash'>
	wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz		wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz
			</source>

	It was compiled from source (using gcc4.8.1) on 03-02-2015:		It was compiled from source (using gcc4.8.1) on 03-02-2015:

Megen002: /* Installation details */

2015-02-04T13:49:16Z

Installation details

← Older revision		Revision as of 15:49, 4 February 2015
Line 30:		Line 30:
	== Installation details ==		== Installation details ==

	ALLPATHS-LG was compiled from source (using gcc4.8) on 15-03-~~2014~~:		ALLPATHS-LG 51910 was downloades as 'latest version':
	~~Source was downloaded by choosing the~~ '~~latests~~' ~~link from here:~~		wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz
	~~http:~~/~~/www~~.~~broadinstitute~~.~~org~~/~~software~~/~~allpaths~~-lg/~~blog~~/~~?page_id~~=12
			It was compiled from source (using gcc4.8.1) on 03-02-2015:

			<source lang='bash'>
			module load gcc/4.8.1
			./configure --prefix=/cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910
			make
			make install
			</source>

			Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment.

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

Megen002: Created page with " '''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' is a popular genome assembler. == Module file == The module file can be found in this location:..."

2015-02-04T13:42:45Z

Created page with " '''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' is a popular genome assembler. == Module file == The module file can be found in this location:..."

New page

'''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' 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#######################################################################
## maker ALLPATHS-LG (51910 modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds ALLPATHS-LG (51910) to your environment"
}

module-whatis "Adds ALLPATHS-LG (51910) to your environment"

module load gcc/4.8.1
setenv LC_ALL C

set allpathslg_51910_root /cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910/bin/

prepend-path PATH $allpathslg_51910_root

</source>

== Installation details ==

ALLPATHS-LG was compiled from source (using gcc4.8) on 15-03-2014:
Source was downloaded by choosing the 'latests' link from here:
http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12

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

== External links ==
* [http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG home page]