I had the same problem with deeptools, I guess the original bzip2 package (in anaconda) was built incorrectly because it contains libbz2.a instead of the shared library libbz2.so.1.0
Not sure what is the problem because the recipe seems to be ok (https://github.com/ContinuumIO/anaconda-recipes/blob/master/bzip2/build.sh)
I didn 't want to change anything out of the conda environment so what I did for the moment is build the bzip2 package with shared libraries locally:

Download and extract http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
make -f Makefile-libbz2_so
and then copy the libbz2.so that it creates to deeptools_env/lib

I'm just mentioning this but of course is not the correct solution, it is just so that you can solve it in the meantime while we wait for someone to explain what can be wrong with the bzip2 package.


From: "Previti" <christopher.previti@dkfz-heidelberg.de>
To: "galaxy-dev" <galaxy-dev@lists.galaxyproject.org>
Sent: Wednesday, July 5, 2017 2:51:32 PM
Subject: [galaxy-dev] DeepTools python dependency issues?

Dear all,

I was wondering if anybody has seen the following error after installing deeptools in the galaxy interface:

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/bin/plotCoverage", line 4, in <module>
    from deeptools.plotCoverage import main
  File "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/plotCoverage.py", line 15, in <module>
    import deeptools.countReadsPerBin as countR
  File "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/countReadsPerBin.py", line 9, in <module>
    import deeptools.utilities
  File "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/utilities.py", line 3, in <module>
    import pysam
  File "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/pysam/__init__.py", line 5, in <module>
    from pysam.libchtslib import *
ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory

Has anybody encountered this error before and were you able to resolve it?

Thanks and best regards,

Christopher Previti


Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434


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