date:20180918

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 
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der bestimmungsgem??e Empf?nger sein, kontaktieren Sie bitte den Absender und 
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Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist 
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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/
>
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>   http://galaxyproject.org/search/
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Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

2018-09-18 Thread Peter van Heusden

Yes that was my conclusion, thanks Peter.

As a result I switched to a new table named (shapeit2_ref) and a new tool
name (data_manager_shapeit2_reference) and from planemo side upload seemed
to succeed but the tool is in an error state. I resorted to manually
editing the tool-data table.

Data managers are a bit of an ugly duckling part of Galaxy - not receiving
as much love as other kinds of tools.

Peter


On Tue, 18 Sep 2018 at 14:22 Peter Cock  wrote:

> Hi Peter vH,
>
> I wonder if adding columns is not supported - because some tools
> would define the table without the extra column? You might have
> to define a new data table instead (with largely the same content).
> But to be clear, I am not an expert in this area of Galaxy.
>
> However, it does seem the IUC could lay out some *.loc file best
> practises for tool authors. There is currently a TODO entry here:
>
>
> https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#data-managers
>
> Peter C.
>
> On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden 
> wrote:
>
>> A bit more tracing leads me to suspect that what is happening is that a
>> merge is being called here:
>>
>>
>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/data/__init__.py#L120
>>
>> from:
>>
>>
>> https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/tools/data_table_manager.py#L88
>>
>> i.e. the toolshed maintains an in-memory copy of tool-data tables and if
>> the list of columns in an incoming tool-data table is not the same as the
>> in-memory version the error I saw happens.
>>
>> Which leaves me with the question: how is one meant to update the column
>> list of a tool data table?
>>
>> Peter
>>
>>
>>
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Re: [galaxy-dev] Update from 17.10 to 18.05

2018-09-18 Thread Dannon Baker

Can you look and see which resources are failing to load?  That'd help me
figure out what's going on here.  If you have any local changes to the
interface you will need to run 'make client-production' from the root of
the repository (which should be safe to do in any event, and will rebuild
the entire client application).

On Tue, Sep 18, 2018 at 7:48 AM Jochen Bick 
wrote:

> Hi,
>
> today we tried to update from 17.10 to 18.05
>
> your server is running but with out any interface, its just white after
> loading?
>
> 
> Galaxy
> | AP - Group
> 
> 
>  media="screen" rel="stylesheet" type="text/css" />
>  href="/static/style/jquery-ui/smoothness/jquery-ui.css?v=1537264325"
> media="screen" rel="stylesheet" type="text/css" />
>  rel="stylesheet" type="text/css" />
>  media="screen" rel="stylesheet" type="text/css" />
>
>
> # tail ./galaxy-dist/dsmerror.log
> 09/05/2018 11:18:21 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:18:22 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:19 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from
> lstat, errno = 6
> 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from
> GetFSInfo:stat, errno = 6
> 09/05/2018 11:57:40 ANS1999E Incremental processing of '/' stopped.
>
> Cheers Jochen
> ___
> 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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Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

2018-09-18 Thread Peter Cock

Hi Peter vH,

I wonder if adding columns is not supported - because some tools
would define the table without the extra column? You might have
to define a new data table instead (with largely the same content).
But to be clear, I am not an expert in this area of Galaxy.

However, it does seem the IUC could lay out some *.loc file best
practises for tool authors. There is currently a TODO entry here:

https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#data-managers

Peter C.

On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden  wrote:

> A bit more tracing leads me to suspect that what is happening is that a
> merge is being called here:
>
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/data/__init__.py#L120
>
> from:
>
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/tools/data_table_manager.py#L88
>
> i.e. the toolshed maintains an in-memory copy of tool-data tables and if
> the list of columns in an incoming tool-data table is not the same as the
> in-memory version the error I saw happens.
>
> Which leaves me with the question: how is one meant to update the column
> list of a tool data table?
>
> Peter
>
>
>
___
Please keep all replies on the list by using "reply all"
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[galaxy-dev] Update from 17.10 to 18.05

2018-09-18 Thread Jochen Bick

Hi,

today we tried to update from 17.10 to 18.05

your server is running but with out any interface, its just white after
loading?


Galaxy
| AP - Group








# tail ./galaxy-dist/dsmerror.log
09/05/2018 11:18:21 ANS0361I DIAG: TransErrno: Unexpected error from
GetFSInfo:stat, errno = 6
09/05/2018 11:18:22 ANS0361I DIAG: TransErrno: Unexpected error from
GetFSInfo:stat, errno = 6
09/05/2018 11:57:19 ANS0361I DIAG: TransErrno: Unexpected error from
GetFSInfo:stat, errno = 6
09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from
GetFSInfo:stat, errno = 6
09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from
GetFSInfo:stat, errno = 6
09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from
lstat, errno = 6
09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from
GetFSInfo:stat, errno = 6
09/05/2018 11:57:40 ANS1999E Incremental processing of '/' stopped.

Cheers Jochen
___
Please keep all replies on the list by using "reply all"
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[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
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[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

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

Re: [galaxy-dev] Update from 17.10 to 18.05

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

[galaxy-dev] Update from 17.10 to 18.05

[galaxy-dev] Issue with deseq2

[galaxy-dev] Issue with deseq2

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