Issue with deseq2

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Issue with deseq2

Previti

Dear all,

I have been trying to get deseq2 (latest version 17,  2018-09-05 from iuc; we are still running on galaxy version 17.09) to work properly but to no avail. Older versions have other errors, I have focused on the latest version.

I get this cryptic error when I run it:

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
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 42-4661

christopher.previti@...
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.



    

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Issue with deseq2

Previti
Dear all,

I have been trying to get deseq2 (latest version 17,  2018-09-05 from iuc; we are still running on galaxy version 17.09) to work properly but to no avail. Older versions have other errors, I have focused on the latest version.

I get this cryptic error when I run it:

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
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 42-4661

christopher.previti@...
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:
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Re: Issue with deseq2

Marius van den Beek
Hi Christopher,

due to the old version of Galaxy you need to manually update Conda (conda update conda)
and explicitly set the current channel order in your galaxy.ini file, this should be
conda_ensure_channels = iuc,conda-forge,bioconda,defaults

With these set you can remove the exisiting conda environment for deseq2
(conda env remove -n mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101)
and then re-install deseq2.
Once you update to a newer Galaxy version you can comment the conda_ensure_channels setting again
and continue using the default channel order that Galaxy ships.

Hope that helps,
Marius


On Tue, 18 Sep 2018 at 12:18, Christopher Previti <[hidden email]> wrote:
Dear all,

I have been trying to get deseq2 (latest version 17,  2018-09-05 from iuc; we are still running on galaxy version 17.09) to work properly but to no avail. Older versions have other errors, I have focused on the latest version.

I get this cryptic error when I run it:

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
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 42-4661

christopher.previti@...
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/

___________________________________________________________
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:
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Re: Issue with deseq2

Previti
Thanks a lot!
I got it to work exactly as you said.
Cheers,
Christopher

On Sep 18, 2018, at 15:56, Marius van den Beek <[hidden email]> wrote:

Hi Christopher,

due to the old version of Galaxy you need to manually update Conda (conda update conda)
and explicitly set the current channel order in your galaxy.ini file, this should be
conda_ensure_channels = iuc,conda-forge,bioconda,defaults

With these set you can remove the exisiting conda environment for deseq2
(conda env remove -n mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101)
and then re-install deseq2.
Once you update to a newer Galaxy version you can comment the conda_ensure_channels setting again
and continue using the default channel order that Galaxy ships.

Hope that helps,
Marius


On Tue, 18 Sep 2018 at 12:18, Christopher Previti <[hidden email]> wrote:
Dear all,

I have been trying to get deseq2 (latest version 17,  2018-09-05 from iuc; we are still running on galaxy version 17.09) to work properly but to no avail. Older versions have other errors, I have focused on the latest version.

I get this cryptic error when I run it:

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R: symbol lookup error: 
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined symbol: PC

Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
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 42-4661

christopher.previti@...
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/

___________________________________________________________
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/