Difference between revisions of "Trinity"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
Moskalenko (talk | contribs) m (Text replace - "]] {| <!--Main settings - REQUIRED-->" to "]] {|<!--Main settings - REQUIRED-->") |
||
| Line 2: | Line 2: | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
[[Category:Bioinformatics]][[Category:Software]] | [[Category:Bioinformatics]][[Category:Software]] | ||
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|trinity}} | |{{#vardefine:app|trinity}} | ||
|{{#vardefine:url|http://trinityrnaseq.sourceforge.net/}} | |{{#vardefine:url|http://trinityrnaseq.sourceforge.net/}} | ||
Revision as of 18:11, 10 August 2012
|
|
Description
Trinity contains three applications - Inchworm, Chrysalis, and Butterfly.
How To Run
To run Trinity after you load the module use the "Trinity.pl" perl script, or run_Trinity.sh shell script, which is particularly useful as the optional ALLPATHS-LG software is enabled at UF HPC.
If the run produces an error that states that java could not create a virtual machine due to insufficient heap memory you can set the java memory with an
export _JAVA_OPTIONS="-Xmx2g"
command either at the command line if doing an interactive run on a test node or in the job script. Make sure that the value in the "-Xmx" is less then the amount of memory you requested from the batch system.