Hi 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. cheers, Ignacio > From: "Previti" <christopher.prev...@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 [ > > mailto:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/bin/plotCoverage > | > > "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/bin/plotCoverage" > ] , line 4, in <module> > from deeptools.plotCoverage import main > File [ > > mailto:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/plotCoverage.py > | > > "/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 [ > > mailto:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/countReadsPerBin.py > | > > "/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 [ > > mailto:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/utilities.py > | > > "/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 [ > > mailto:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/pysam/__init__.py > | > > "/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) > Bioinformatician > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > Room: B2.102 (INF580/TP3) > Phone: +49 6221 42-4434 > [ http://www.dkfz.de/ | christopher.prev...@dkfz.de ] > [ http://www.dkfz.de/ | www.dkfz.de ] > Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta > VAT-ID No.: DE143293537 > Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen > bestimmt, an die sie adressiert ist. > Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte > Informationen > enthalten. Sollten Sie nicht > der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und > löschen Sie die Mitteilung. > Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist > untersagt. > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/
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