Installing software on marvin - Revision history

Jw297 at 13:33, 17 September 2018

2018-09-17T13:33:14Z

Jw297 at 13:32, 17 September 2018

2018-09-17T13:32:12Z

Jw297 at 09:51, 24 January 2018

2018-01-24T09:51:23Z

Jw297 at 09:33, 24 January 2018

2018-01-24T09:33:45Z

Jw297: /* Installing software on Marvin/Module */

2018-01-24T09:32:57Z

‎Installing software on Marvin/Module

Jw297: Created page with "=Installing software on Marvin/Module= Software needs to be installed in: /usr/local/Modules/modulefiles/tools/// to make use of the modules f..."

2018-01-23T15:45:25Z

Created page with "=Installing software on Marvin/Module= Software needs to be installed in: /usr/local/Modules/modulefiles/tools/<software name>/<version number>/ to make use of the modules f..."

New page

=Installing software on Marvin/Module=

Software needs to be installed in:
/usr/local/Modules/modulefiles/tools/<software name>/<version number>/
to make use of the modules feature.

The text files that tells modules that the software is there are located in:
/usr/local/Modules/3.2.10/modulefiles/<software>/<version number>

An example of which is below:

#%Module1.0#####################################################################
##
##
proc ModulesHelp { } {
puts stderr "\tStacks - loads Stacks 2.0Beta7c software
\tSoftware available:
\tcstacks
\testacks
\thstacks
\tpstacks
\trxstacks
\tsstacks
\tustacks
"
}

module-whatis "loads Stacks version 1.41 software"

module load perl samtools/0.1.19b sparsehash

# for Tcl script use only
set version 2.0Beta7c
set prefix /usr/local/Modules/modulefiles/tools/stacks/${version}
set sys linux64

setenv STACKSROOTDIR ${prefix}
prepend-path PATH ${prefix}/bin

← Older revision		Revision as of 13:33, 17 September 2018
Line 49:		Line 49:

	./configure CXX=/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ CPP='/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ -E' --prefix=whatever		./configure CXX=/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ CPP='/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ -E' --prefix=whatever
		+
		+	If that doesn't work, use the redhat developer toolset
		+
		+	== Red Hat Developer Toolset ==
		+
		+	Seeing as the cluster runs with RHEL 6 which, though updated continuously, was released in 2011, there are various things it's incapable of. Primary among these is a gcc compiler with the C++ standard C++11, which alot of software is now using. THis requires gcc version 4.8 instead of the 4.4 RHEL6 uses. The solution is the poorly named developer toolset, which Red Hat makes available. To invoke it:
		+
		+	scl enable devtoolset-2 "bash"
		+
		+	This will open a new bash subprocess where the gcc will be version 4.8

← Older revision		Revision as of 13:32, 17 September 2018
Line 43:		Line 43:
	=Removing=		=Removing=
	Move the folder and it's associated module file into /shelf/scratch/root/dustbin_for_modules means we have it ready if we need to restore it.		Move the folder and it's associated module file into /shelf/scratch/root/dustbin_for_modules means we have it ready if we need to restore it.
		+
		+	=Compiling=
		+	The non-standard location of the gcc binaries can cause problems. For configuring, use the line below to help:
		+
		+
		+	./configure CXX=/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ CPP='/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ -E' --prefix=whatever

@@ Line 4: / Line 4: @@
 or
   /shelf/modulefiles/
-to make use of the modules feature. **Beware** using /usr/local/Modules/ as there's only 50Gb of space on /. Use /shelf/modulefiles/ for anything big (I'm looking at you interproscan).
+to make use of the modules feature. '''Beware''' using /usr/local/Modules/ as there's only 50Gb of space on /. Use /shelf/modulefiles/ for anything big (I'm looking at you interproscan).
 The text files that tells modules that the software is there are located in:

@@ Line 1: / Line 1: @@
 Software needs to be installed in:
   /usr/local/Modules/modulefiles/tools/<software name>/<version number>/
@@ Line 39: / Line 40: @@
   setenv STACKSROOTDIR ${prefix}
   prepend-path    PATH   		${prefix}/bin