driver identification using CHASM in cancer

[libiyagirl]

Hello,

I am trying to run CHASM "BuildClassifier" command. But it always return error saying:

Traceback (most recent call last):
File "<string>", line 31, in <module>
File "/home/andywong86/pyinstaller-1.4/iu.py", line 436, in importHook
File "/home/andywong86/pyinstaller-1.4/iu.py", line 521, in doimport
File "./build/pyi.linux2/BuildClassifier/outPYZ1.pyz/util.makemuts", line 23, in <module>
File "./build/pyi.linux2/BuildClassifier/outPYZ1.pyz/util.genes", line 59, in __init__
IOError: [Errno 2] No such file or directory: './ClassifierPack/refseq.info'

I don't know what's happening. Anyone used CHASM before?

Thank you very much!

[nyk]

I assume you have to set the CHASMDIR evironment variable, because I got a similar error when I did not do that, if I remember correctly.
Because I'm going to use CHASM from a script, I add the setting of that variable before the BuildClassifier command. Like this:
CHASMDIR=/opt/CHASM /opt/CHASM/BuildClassifier -m /opt/CHASM/ClassifierPack/contexts/BR.context -i /opt/CHASM/ClassifierPack/calibrate.tmps -o breast_cancer

I also have a question:
Is it the idea to use the "calibrate" set of mutations for building the classifier, like I did in the above command? And then use RunChasm on the mutation-list of cancer samples I want to test?
Or should the model be calibrated on the *same* set of mutations I will use RunChasm on?