Thanks, I'll give it a try!
Cheers,
Christopher
On 07/05/2017 03:13 PM, Ignacio EGUINOA wrote:
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.previti(a)dkfz-heidelberg.de>
*To: *"galaxy-dev" <galaxy-dev(a)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(a)2.5.1/bin/plotCoverage",
line 4, in <module>
from deeptools.plotCoverage import main
File
"/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools(a)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(a)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(a)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(a)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
christopher.previti(a)dkfz.de <
http://www.dkfz.de/>
www.dkfz.de <
http://www.dkfz.de/>
Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
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--
*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
christopher.previti(a)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.