Help Needed To Run Seal For Genome Mapping.

Question

[bashwin.u]

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

Answer 1

[Roman Valls Guimerà]

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.

[bashwin.u]

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?

[Roman Valls Guimerà]

You have to install HADOOP separately, afaik Seal assumes that you have an already running and configured HADOOP cluster, check the docs: http://biodoop-seal.sourceforge.net/installation_generic.html#installation-generic