System-specific installation issues (and possible solution?)

[Álvaro Andrades Delgado]

Hi,

I have been trying to install OncoDriveFML in my cluster (Red Hat Enterprise Linux Server, release 6.4). I have tried conda and pip. The installation proceeds without errors, but when I run oncodrivefml I get the following error:

Traceback (most recent call last):
  File "<my_directory>/anaconda3/bin/oncodrivefml", line 6, in <module>
    from oncodrivefml.main import cmdline
  File "<my_directory>/anaconda3/lib/python3.7/site-packages/oncodrivefml/main.py", line 16, in <module>
    from oncodrivefml.oncodrivefml import OncodriveFML
  File "<my_directory>/anaconda3/lib/python3.7/site-packages/oncodrivefml/oncodrivefml.py", line 18, in <module>
    from oncodrivefml.executors.bymutation import GroupByMutationExecutor
  File "<my_directory>/anaconda3/lib/python3.7/site-packages/oncodrivefml/executors/bymutation.py", line 3, in <module>
    from oncodrivefml.executors.element import ElementExecutor
  File "<my_directory>/anaconda3/lib/python3.7/site-packages/oncodrivefml/executors/element.py", line 8, in <module>
    from oncodrivefml.scores import Scores
  File "<my_directory>/anaconda3/lib/python3.7/site-packages/oncodrivefml/scores.py", line 38, in <module>
    import tabix
ImportError: <my_directory>/anaconda3/lib/python3.7/site-packages/tabix.cpython-37m-x86_64-linux-gnu.so: undefined symbol: PyString_FromStringAndSize

I have tried to install OncoDriveFML in other machines following the exact same steps and I do not get this error message. I believe this error might be related to a tabix issue reported here, according to which the installation flags for the compiler were in a wrong order. It seems to be fixed in later versions of tabix. I googled a bit more and these issues do indeed seem to arise due to the order of the compiler flags.

Could this issue be fixed, maybe by requiring a later tabix version? (assuming this is the real cause of the error).

Thank you!

[Iker Reyes]

OncodriveFML is using pytabix and we are using the latest release (note that release 0.0.2 is later than 0.1 in their repository). Could you try in a Python 3.6 environment?

If you are aware of any other Python wrapper for tabix that does not have this issue (e.g. pysam) we might consider using that in the future.

[Álvaro Andrades Delgado]

Thank you for your quick reply.

I installed OncoDriveFML in a Python 3.6 environment but the error was the same. Unfortunately, I do not know about any other wrappers for tabix that may not have this issue.

I did some more checks and Python is unable to import tabix in my system, so it seems to be a tabix issue after all.

[Iker Reyes]

It is a bit weird, because at least in CentOS 7 it is working (and there should not be much difference between CentOS and RHEL). Can you run Docker or Singularity in your system? This way we might be able to containerize the application and hopefully it works.

‌

[Álvaro Andrades Delgado]

Thank you again and I apologize for taking so long to reply.

I have been trying to install Docker or Singularity in my university’s cluster, but unfortunately the kernel is incompatible with either of them (the kernel is much older than the absolute minimum version required for either Docker or Singularity to run).

I am not sure if there is much more that we can do at this point. It must be some obscure system-specific problem that might be solved by updating the software, which unfortunately I cannot do.

Thank you again for your time.