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Help Needed To Run Seal For Genome Mapping.

Hello, I managed to build an index file from the reference genome using Seal. Now I am trying to run Seqal but I am running into errors.

./seqal /user/hadoop/seal/synthetic_prq1 /user/hadoop/seal_output /mnt/shared/data/version0.5.x/index.tar
Traceback (most recent call last):
File "./seqal", line 39, in <module>
from bl.mr.seq.seqal.seqal_run import SeqalRun
File "/mnt/shared/seal-0.3.2-src/build/bl/mr/seq/seqal/__init__.py", line 25, in <module>
from pydoop.pipes import runTask, Factory
ImportError: No module named pydoop.pipes

I have a hadoop cluster of 1 master and 5 slaves (Version 1.0.3). I have installed pydoop on the shared nfs folder in the cluster.

Can anyone please tell me how to get past this error?

Thanks, Ashwin

genome mapping paired-end
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updated by Roman Valls Guimerà Roman Valls Guimerà • written by bashwin.u • bashwin.u

1 answer

Sounds like you need to set your PYTHONPATH environment variable to point to that nfs folder you mention.

Alternatively, I think it's best if you install a python virtualenv by using virtualenv-burrito:

https://github.com/brainsik/virtualenv-burrito

And then, create a virtualenv with mkvirtualenv and then you can install everything by just running pip install seal.

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written by Roman Valls Guimerà Roman Valls Guimerà

I have set PYTHONPATH. Still its not working. I installed and created a virtualenv. But I am running into errors when I run pip install seal. error: Could not build Java components. Any idea what may be the reason for this? Also I have a doubt. This command pip install seal, are these packages related to the ngs application seal?

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written by bashwin.u • bashwin.u

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