subject:"\[galaxy\-dev\] Issue with deseq2"

Re: [galaxy-dev] Issue with deseq2

2018-09-18 Thread Previti, Christopher

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 
mailto:m.vandenb...@gmail.com>> 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 
mailto:christopher.prev...@dkfz-heidelberg.de>>
 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.prev...@dkfz.de
www.dkfz.de
Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschlie?lich f?r die Personen 
bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur f?r den/die Empf?nger bestimmte 
Informationen enthalten. Sollten Sie nicht
der bestimmungsgem??e Empf?nger sein, kontaktieren Sie bitte den Absender und 
l?schen 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/

Re: [galaxy-dev] Issue with deseq2

2018-09-18 Thread 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 <
christopher.prev...@dkfz-heidelberg.de> 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.prev...@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/
___
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] Issue with deseq2

2018-09-18 Thread Christopher 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

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.prev...@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/

[galaxy-dev] Issue with deseq2

2018-09-18 Thread Previti

Dear all,

I get this cryptic error when I run it:

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.prev...@dkfz.de
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/

Re: [galaxy-dev] Issue with deseq2

Re: [galaxy-dev] Issue with deseq2

[galaxy-dev] Issue with deseq2

[galaxy-dev] Issue with deseq2

4 matches

Site Navigation

Mail list logo

Footer information