Hi all,
trying to install the deeptools_suite from the toolshed I only get the following error:
"500 Internal Server Error
nginx/1.11.10"
This happens as well for the dependencies, e.g. deeptools_bigwig_compare.
I am currently using Galaxy 16.10 with nginx proxy.
Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency:
"Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433."
Has anyone seen these problems before and knows a solution?
Best regards, Timo Janßen
Hi Timo,
Use conda for dependency resolution in Galaxy and make your life easier :)
Devon
On 03/08/2017 06:31 PM, Timo Janßen wrote:
Hi all,
trying to install the deeptools_suite from the toolshed I only get the following error:
"500 Internal Server Error
nginx/1.11.10"
This happens as well for the dependencies, e.g. deeptools_bigwig_compare.
I am currently using Galaxy 16.10 with nginx proxy.
Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency:
"Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433."
Has anyone seen these problems before and knows a solution?
Best regards, Timo Janßen
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/mailinglists/
Hi Devon,
I'm also experiencing similar issues. Could you please briefly explain how to use Condo with Galaxy?
Is there any other versions where Conda is integrated apart from the regular Galaxy distributions?
On Mar 8, 2017 7:38 PM, "Devon Ryan" dpryan79@gmail.com wrote:
Hi Timo,
Use conda for dependency resolution in Galaxy and make your life easier :) Devon
On 03/08/2017 06:31 PM, Timo Janßen wrote:
Hi all,
trying to install the deeptools_suite from the toolshed I only get the following error:
"500 Internal Server Error
nginx/1.11.10"
This happens as well for the dependencies, e.g. deeptools_bigwig_compare.
I am currently using Galaxy 16.10 with nginx proxy.
Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency:
"Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433."
Has anyone seen these problems before and knows a solution?
Best regards, Timo Janßen
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/mailinglists/
-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79@gmail.com
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/
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The documentation here is quite good: https://docs.galaxyproject.org/en/master/admin/conda_faq.html
As an aside, the dockerized version of Galaxy (https://github.com/bgruening/docker-galaxy-stable) from Björn Gruening makes this convenient.
Devon
On 03/08/2017 08:55 PM, Md. Rezaul Karim wrote:
Hi Devon,
I'm also experiencing similar issues. Could you please briefly explain how to use Condo with Galaxy?
Is there any other versions where Conda is integrated apart from the regular Galaxy distributions?
On Mar 8, 2017 7:38 PM, "Devon Ryan" <dpryan79@gmail.com mailto:dpryan79@gmail.com> wrote:
Hi Timo, Use conda for dependency resolution in Galaxy and make your life easier :) Devon On 03/08/2017 06:31 PM, Timo Janßen wrote:Hi all, trying to install the deeptools_suite from the toolshed I only get the following error: "500 Internal Server Error nginx/1.11.10" This happens as well for the dependencies, e.g. deeptools_bigwig_compare. I am currently using Galaxy 16.10 with nginx proxy. Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency: "Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433." Has anyone seen these problems before and knows a solution? Best regards, Timo Janßen ___________________________________________________________ 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/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email:dpryan79@gmail.com <mailto:dpryan79@gmail.com> ___________________________________________________________ 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/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
On 03/08/2017 08:38 PM, Devon Ryan wrote:
Hi Timo,
Use conda for dependency resolution in Galaxy and make your life easier :)
Devon
Hi Devon,
thanks for the suggestion. I think that wasn't the actual issue but I managed to solve it now. I installed DeepTools via the command line api and despite getting errors all tools have been installed. The matplotlib package still complains about the missing dependency but seems to work anyhow.
Timo
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
Try installing libbz2-dev (or whatever that's called on your system), since it's not in the normal conda channels.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Wed, Jul 5, 2017 at 2:51 PM, Previti christopher.previti@dkfz-heidelberg.de wrote:
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) 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@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/
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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@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.previti@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/
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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@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) 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@dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://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/
It worked, thanks again!
On 07/05/2017 03:37 PM, Previti wrote:
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@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) 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@dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://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/-- *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@dkfz.de http://www.dkfz.de/ www.dkfz.de http://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/
galaxy-dev@lists.galaxyproject.org
-
Devon Ryan -
Devon Ryan -
Ignacio EGUINOA -
Md. Rezaul Karim -
Previti -
Timo Janßen