Allpathslg 51910: Difference between revisions
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/cm/shared/modulefiles/SHARED/ | /cm/shared/modulefiles/SHARED/ | ||
< | <pre> | ||
#%Module1.0####################################################################### | #%Module1.0####################################################################### | ||
## maker ALLPATHS-LG (51910 modulefile | ## maker ALLPATHS-LG (51910 modulefile | ||
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</ | </pre> | ||
== Installation details == | == Installation details == | ||
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ALLPATHS-LG 51910 was downloades as 'latest version': | ALLPATHS-LG 51910 was downloades as 'latest version': | ||
< | <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 | ||
</ | </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: | ||
< | <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 | ||
</ | </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: | |||
<pre> | |||
wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz | |||
</pre> | |||
== See also == | == See also == | ||
Latest revision as of 15:41, 15 June 2023
ALLPATHS-LG is a popular genome assembler.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
#%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
Installation details
ALLPATHS-LG 51910 was downloades as 'latest version':
wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz
It was compiled from source (using gcc4.8.1) on 03-02-2015:
module load gcc/4.8.1 ./configure --prefix=/cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910 make make install
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:
wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz