Blat v35: Difference between revisions
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'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome. | '''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome. | ||
== Module file == | == Module file == | ||
The module file can be found in this location: | The module file can be found in this location: | ||
/cm/shared/ | /cm/shared/modulefiles/SHARED/ | ||
<source lang='tcl'> | <source lang='tcl'> | ||
| Line 22: | Line 17: | ||
module-whatis "Adds the entire blat suite (v35) including blat tools (2013-20-12 download) to your environment" | module-whatis "Adds the entire blat suite (v35) including blat tools (2013-20-12 download) to your environment" | ||
set blat_root /cm/shared/apps/ | set blat_root /cm/shared/apps/SHARED/blat/blat-v35/blat | ||
set blat_tools_root /cm/shared/apps/ | set blat_tools_root /cm/shared/apps/SHARED/blat/blat-v35 | ||
prepend-path PATH $blat_tools_root | prepend-path PATH $blat_tools_root | ||
prepend-path PATH $blat_root | prepend-path PATH $blat_root | ||
</source> | |||
== Installation details == | |||
The entire suite of binaries/executable was downloaded on 20-12-2013: | |||
<source lang='bash'> | |||
rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./ | |||
</source> | </source> | ||
== See also == | == See also == | ||
* [[Globally_installed_software | Globally installed software]] | |||
* [[ABGC_modules | ABGC specific modules]] | |||
== External links == | == External links == | ||
* [http:// | * [http://genome.ucsc.edu/FAQ/FAQblat.html Blat at UCSC] | ||
* [http:// | * [http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Download page of 64-bit executables for Linux] | ||
Latest revision as of 09:56, 15 March 2014
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
<source lang='tcl'>
- %Module1.0#######################################################################
- blat suite (v35) plus tools (2013-20-12 download) modulefile
proc ModulesHelp { } {
puts stderr "\tAdds the entire blat suite (v35) including blat tools (2013-20-12 download) to your environment"
}
module-whatis "Adds the entire blat suite (v35) including blat tools (2013-20-12 download) to your environment"
set blat_root /cm/shared/apps/SHARED/blat/blat-v35/blat set blat_tools_root /cm/shared/apps/SHARED/blat/blat-v35 prepend-path PATH $blat_tools_root prepend-path PATH $blat_root
</source>
Installation details
The entire suite of binaries/executable was downloaded on 20-12-2013: <source lang='bash'> rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./ </source>