OSU HPC Software

As we get stuff installed that isn't in a default path, we're using env. modules.  So just:

module load bio_apps 

will bring everything in the path.  I'd really like to do a sample test of these so we can verify they work...

*Picard requires Java 1.6.0, which necessitates prepending the proper directory to a user’s path. Picard is run with a command in the form of “java -jar /share/apps/picard/1.74/nameofpicardcommand.jar.”

1. bwa  -done
2. bedtools  -done
3. samtools -done
4. picard -done
5. icommands -done  (users can just type iinit and only need their iplant creds)
6. velvet -done
7. tophat -done
8. bowtie -done
9. igvtools - NOT done - please advise if you plan to use the CLI version or just the GUI in atmosphere or somewhere else.
10. R (maybe) -done
11. perl 5.12.x - have perl version 5.12.3
12. python 2.7.x - have python version 2.7.2 and it has mjson.tool... 
    1. Just need a version of python where the following command line gives this result, rather than "python: module json.tool not found"

       echo "hello" | python -mjson.tool
       No JSON object could be decoded

13. wget - done
14. curl - done 
15. fastx_toolkit  done
16.  

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