9:13 a.m.
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 [
mailto:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/bin/plotCoverage
|
"/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools(a)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(a)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(a)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(a)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(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
Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537
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