Re: [galaxy-dev] Input paired dataset collection in workflow

2019-01-24 Thread Christopher Previti 

I got it, sorry to bother you.
One can actually specify the type of collection...and set it to list of 
dataset pairs.

Best regards,
Christopher


Am 24.01.19 um 10:19 schrieb Christopher Previti:


Dear Galaxy Community,

Is there a way to input a paired dataset collection into a workflow?

I would like to build a workflow using cutadapt with a paired dataset 
collection but...I'm missing something.


I have seen workflows (at usegalaxy.eu for example: 
1_CLIPseq-Explorer_demulti_PEAKachu_iCLIP_hg19) where this is possible.


But how is this done practically?

Thanks and best regards,

Christopher


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.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <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 
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--
*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.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <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.



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[galaxy-dev] Input paired dataset collection in workflow

2019-01-24 Thread Christopher Previti 

Dear Galaxy Community,

Is there a way to input a paired dataset collection into a workflow?

I would like to build a workflow using cutadapt with a paired dataset 
collection but...I'm missing something.


I have seen workflows (at usegalaxy.eu for example: 
1_CLIPseq-Explorer_demulti_PEAKachu_iCLIP_hg19) where this is possible.


But how is this done practically?

Thanks and best regards,

Christopher


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

logo 

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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[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

/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 <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.



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Re: [galaxy-dev] Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused

2017-01-17 Thread Christopher Previti 

Thanks a lot, it works now!


Am 17.01.2017 um 16:45 schrieb Nate Coraor:

Hi Christopher,

It's been up for a while now. The IP address is now 128.118.250.24 - 
is it still resolving to 128.118.250.10 for you?


--nate

On Mon, Jan 16, 2017 at 3:01 AM, Christopher Previti 
<christopher.prev...@dkfz-heidelberg.de 
<mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:


Hi Nate,
Happy New Year (though belated)! I was wondering if you managed to
get the rsync server to work...it still gives me the same error
message I received
the last time I tried.

Cheers and thanks!
Christopher



Am 19.12.2016 um 18:30 schrieb Nate Coraor:

Hi Christopher,

It's currently down due to a hardware failure. I hope to have it
back up within the week. Sorry for the inconvenience.

Thanks,
--nate

On Wed, Dec 14, 2016 at 3:14 AM, Christopher Previti
<christopher.prev...@dkfz-heidelberg.de
<mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:

Dear all,

I was wondering if anybody was able to get the rsync server
datacache.g2.bx.psu.edu <http://datacache.g2.bx.psu.edu> to
work? Have there been non-documented changes?

We still get following messages:

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX
<http://datacache.g2.bx.psu.edu/indexes/phiX> .
rsync: failed to connect to datacache.g2.bx.psu.edu
<http://datacache.g2.bx.psu.edu> (128.118.250.10): Connection
refused (111)
rsync error: error in socket IO (code 10) at
clientserver.c(128) [Receiver=3.1.1]

My colleague Georgios Nikolis and I are working on a local
Galaxy installation at the DKFZ and would really like to use
the pre-built indices.

    Cheers,

Christopher Previti



 Weitergeleitete Nachricht 
Betreff:Fwd: [galaxy-dev] Usegalaxy.org Data Rsync
Connection refused
Datum:  Tue, 13 Dec 2016 13:46:48 +0100
Von:Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
<mailto:g.niko...@dkfz-heidelberg.de>
An: Christopher Previti
<christopher.prev...@dkfz-heidelberg.de>
<mailto:christopher.prev...@dkfz-heidelberg.de>





*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659 <tel:+49%206221%20424659>

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

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





 Forwarded Message 
Subject:[galaxy-dev] Usegalaxy.org Data Rsync Connection
refused
Date:   Fri, 28 Oct 2016 15:23:14 +0200
From:   Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
<mailto:g.niko...@dkfz-heidelberg.de>
To: galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>
<galaxy-dev@lists.galaxyproject.org>
<mailto:galaxy-dev@lists.galaxyproject.org>



Dear all,
we are currently working on setting up a new local Galaxy
installation and I would like to obtain the genome reference
data available on the public Galaxy instance. I am following
the instructions on the Wiki page
(https://wiki.galaxyproject.org/Admin/UseGalaxyRsync
<https://wiki.galaxyproject.org/Admin/UseGalaxyRsync>), but I
can't seem to be able to access datacache.g2.bx.psu.edu
<http://datacache.g2.bx.psu.edu> via rsync.
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX
<http://datacache.g2.bx.psu.edu/indexes/phiX> .
rsync: failed to connect to datacache.g2.bx.psu.edu
<http://datacache.g2.bx.psu.edu> (128.118.250.10): Connection
refused (111)
rsync error: error in socket IO (code 10) at
clientserver.c(128) [Receiver=3.1.1]

Does anyone know if the URL has changed in the meantime? Is
there any alternative way to access this data?

Thanks in advance!

Best regards,
Georgios


-- 
*Georgios Nikolis*

Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659 <te

[galaxy-dev] Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused

2016-12-14 Thread Christopher Previti 

Dear all,

I was wondering if anybody was able to get the rsync server 
datacache.g2.bx.psu.edu to work? Have there been non-documented changes?


We still get following messages:

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): 
Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(128) 
[Receiver=3.1.1]


My colleague Georgios Nikolis and I are working on a local Galaxy 
installation at the DKFZ and would really like to use the pre-built indices.


Cheers,

Christopher Previti



 Weitergeleitete Nachricht 
Betreff:Fwd: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused
Datum:  Tue, 13 Dec 2016 13:46:48 +0100
Von:Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
An: Christopher Previti <christopher.prev...@dkfz-heidelberg.de>





*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

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





 Forwarded Message 
Subject:[galaxy-dev] Usegalaxy.org Data Rsync Connection refused
Date:   Fri, 28 Oct 2016 15:23:14 +0200
From:   Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
To: 	galaxy-dev@lists.galaxyproject.org 
<galaxy-dev@lists.galaxyproject.org>




Dear all,
we are currently working on setting up a new local Galaxy installation 
and I would like to obtain the genome reference data available on the 
public Galaxy instance. I am following the instructions on the Wiki page 
(https://wiki.galaxyproject.org/Admin/UseGalaxyRsync), but I can't seem 
to be able to access datacache.g2.bx.psu.edu via rsync.

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): 
Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(128) 
[Receiver=3.1.1]


Does anyone know if the URL has changed in the meantime? Is there any 
alternative way to access this data?


Thanks in advance!

Best regards,
Georgios


--
*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef 
Puchta

VAT-ID No.: DE143293537





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