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elzbth / jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
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Adding Pandas dependency #1

Closed samfux84 closed 8 years ago

samfux84 commented 8 years ago

Dear Jitterbug developer,

as dependencies for jitterbug, you mention pysam, pybedtools and psutil. I have installed all of these modules and then tried to run jitterbug, which resulted in an error message about pandas not being installed.

[sfux@develop01 09032016]$ ./jitterbug.py -h
Traceback (most recent call last):
  File "./jitterbug.py", line 21, in <module>
    from Run_TE_ID_reseq import *
  File "/cluster/apps/gdc/jitterbug/09032016/Run_TE_ID_reseq.py", line 7, in <module>
    from BamReader import *
  File "/cluster/apps/gdc/jitterbug/09032016/BamReader.py", line 2, in <module>
    import pybedtools
  File "/cluster/apps/gdc/python/2.7.11/lib64/python2.7/site-packages/pybedtools-0.7.6-py2.7-linux-x86_64.egg/pybedtools/__init__.py", line 12, in <module>
    from . import contrib
  File "/cluster/apps/gdc/python/2.7.11/lib64/python2.7/site-packages/pybedtools-0.7.6-py2.7-linux-x86_64.egg/pybedtools/contrib/__init__.py", line 4, in <module>
    from . import long_range_interaction
  File "/cluster/apps/gdc/python/2.7.11/lib64/python2.7/site-packages/pybedtools-0.7.6-py2.7-linux-x86_64.egg/pybedtools/contrib/long_range_interaction.py", line 7, in <module>
    import pandas
ImportError: No module named pandas

Please add also the pandas package in the list of dependencies.

Thank you very much and best regards

Samuel Fux

samfux84 commented 8 years ago

It also requires the Python package memory_profiler:

[sfux@develop01 09032016]$ ./jitterbug.py -h
Traceback (most recent call last):
  File "./jitterbug.py", line 21, in <module>
    from Run_TE_ID_reseq import *
  File "/cluster/apps/gdc/jitterbug/09032016/Run_TE_ID_reseq.py", line 18, in <module>
    from memory_profiler import profile
ImportError: No module named memory_profiler
mbosio85 commented 8 years ago

Thanks for noticing. Now it has been included.