Re: [galaxy-dev] V18.01 'View all histories' doesn't work

2018-05-15 Thread Devon Ryan 
You’ll probably get a more informative error message if you check the logs. 

Sent from my iPhone

> On 15. May 2018, at 17:45, Ping Luo  wrote:
> 
> I just installed Galaxy V18.01. I got an error when clicking 'View all 
> histories' in the history tool bar 
> 
> The error says 'The requested URL /api/histories was not found on this 
> server'.
> 
> 
> Is there anyone experiencing the same problem?
> 
> Ping
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Re: [galaxy-dev] extract extra info (logs) from history

2018-05-02 Thread Devon Ryan 
Sounds like a good excuse to upgrade :)

Sent from my iPhone

> On 2. May 2018, at 16:40, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
> 
> Thanks Devon,
> 
> I think now I got it ;-). We are running 17.05 I might not have the "Summary 
> Options" ? I cannot find them...
> 
> But maybe I can use the flagstat tool for now.
> 
> Cheers Jochen
> 
> 
>> On 02.05.2018 16:34, Devon Ryan wrote:
>> By default the logs are just to stdout. You need to use one of the
>> options (under "Summary Options" on the version on our instance) if
>> you want things saved as a history item.
>> 
>> Devon
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@dpryan.com
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>> 
>> 
>>> On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <jochen.b...@usys.ethz.ch> 
>>> wrote:
>>> That's also an interesting tool. Which gives almost the same result as in
>>> the log file of at HISAT output. I'm not sure why the number of mapped reads
>>> are not 100% identical...
>>> 
>>> but anyway can someone tell me, or maybe Devon did already, where is the log
>>> info of HISAT saved?
>>> 
>>> Cheers Jochen
>>> 
>>> 
>>> 
>>>> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>>> Flagstat might be a good choice here…
>>>> 
>>>> Brad
>>>> 
>>>>> On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
>>>>> 
>>>>> Hi Devon,
>>>>> 
>>>>> do you mean Alignment Summary? How can I access that information and use
>>>>> it for an other tool.
>>>>> 
>>>>> Cheers Jochen
>>>>> 
>>>>> 
>>>>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>>> There are two alignment summary options in the wrapper that will cause
>>>>>> most/all of that to be written to a history item. They're under
>>>>>> "Summary Options".
>>>>>> 
>>>>>> Devon
>>>>>> --
>>>>>> Devon Ryan, Ph.D.
>>>>>> Email: dpr...@dpryan.com
>>>>>> Data Manager/Bioinformatician
>>>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>>>> Stübeweg 51
>>>>>> 79108 Freiburg
>>>>>> Germany
>>>>>> 
>>>>>> 
>>>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.b...@usys.ethz.ch>
>>>>>> wrote:
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>>>> e.g.:
>>>>>>> 26781724 reads; of these:
>>>>>>>26781724 (100.00%) were unpaired; of these:
>>>>>>>  2445411 (9.13%) aligned 0 times
>>>>>>>  20399099 (76.17%) aligned exactly 1 time
>>>>>>>  3937214 (14.70%) aligned >1 times
>>>>>>> 90.87% overall alignment rate
>>>>>>> [bam_sort_core] merging from 21 f
>>>>>>> 
>>>>>>> 
>>>>>>> Is it possible to access these logs?
>>>>>>> 
>>>>>>> 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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>>>>>>>http://galaxyproject.org/search/
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>>>>> http://galaxyproject.org/search/
>>> 
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> 
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Re: [galaxy-dev] extract extra info (logs) from history

2018-05-02 Thread Devon Ryan 
By default the logs are just to stdout. You need to use one of the
options (under "Summary Options" on the version on our instance) if
you want things saved as a history item.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
> That's also an interesting tool. Which gives almost the same result as in
> the log file of at HISAT output. I'm not sure why the number of mapped reads
> are not 100% identical...
>
> but anyway can someone tell me, or maybe Devon did already, where is the log
> info of HISAT saved?
>
> Cheers Jochen
>
>
>
> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>
>> Flagstat might be a good choice here…
>>
>> Brad
>>
>>> On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
>>>
>>> Hi Devon,
>>>
>>> do you mean Alignment Summary? How can I access that information and use
>>> it for an other tool.
>>>
>>> Cheers Jochen
>>>
>>>
>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>
>>>> There are two alignment summary options in the wrapper that will cause
>>>> most/all of that to be written to a history item. They're under
>>>> "Summary Options".
>>>>
>>>> Devon
>>>> --
>>>> Devon Ryan, Ph.D.
>>>> Email: dpr...@dpryan.com
>>>> Data Manager/Bioinformatician
>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>> Stübeweg 51
>>>> 79108 Freiburg
>>>> Germany
>>>>
>>>>
>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.b...@usys.ethz.ch>
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>> e.g.:
>>>>> 26781724 reads; of these:
>>>>>26781724 (100.00%) were unpaired; of these:
>>>>>  2445411 (9.13%) aligned 0 times
>>>>>  20399099 (76.17%) aligned exactly 1 time
>>>>>  3937214 (14.70%) aligned >1 times
>>>>> 90.87% overall alignment rate
>>>>> [bam_sort_core] merging from 21 f
>>>>>
>>>>>
>>>>> Is it possible to access these logs?
>>>>>
>>>>> 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/
>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>http://galaxyproject.org/search/
>>>
>>> ___
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>>>
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>>> http://galaxyproject.org/search/
>
>
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Re: [galaxy-dev] extract extra info (logs) from history

2018-04-26 Thread Devon Ryan 
There are two alignment summary options in the wrapper that will cause
most/all of that to be written to a history item. They're under
"Summary Options".

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
> Hi,
>
> I would like to use the info (log) HISAT is showing, for another tool.
> e.g.:
> 26781724 reads; of these:
>   26781724 (100.00%) were unpaired; of these:
> 2445411 (9.13%) aligned 0 times
> 20399099 (76.17%) aligned exactly 1 time
> 3937214 (14.70%) aligned >1 times
> 90.87% overall alignment rate
> [bam_sort_core] merging from 21 f
>
>
> Is it possible to access these logs?
>
> Cheers Jochen
> ___
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Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

2018-01-11 Thread Devon Ryan 
This is presumably the same question elsewhere:
https://biostar.usegalaxy.org/p/26197/
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Jan 11, 2018 at 9:44 AM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
> Hi Matthias,
>
> sorry for answering so late!
>
> Do you have any error message from the logs during installation?
>
> What means it is not recognised by Galaxy?
> Do you see the conda environment in /tool_deps/_conda/ ?
>
> Is freebayes crashing?
>
> Ciao,
> Bjoern
>
>
>> Dear Galaxy Dev Mailing List,
>>
>> We encountered a problem while installing freebayes and its via Tool
>> Shed.
>>
>> Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19);
>> gawk (4.1.3) (all have the Current Installation Status "Installed
>> through Conda") but then failed on the last dependency "parallel".
>> (Status: "Not Installed")
>>
>> The strange thing is: parallel was installed correctly. Its callable
>> from the command line, (e.g. parallel --help works fine) and
>> installed with the latest version. But it's not recognized by
>> Galaxy.
>>
>> We are using the Galaxy - Docker image in Version 17.09.
>>
>> Can you please assist us in resolving this?
>>
>> Mit freundlichen Grüßen
>>
>> Matthias Enders
>> ---
>>
>>
>>
>> GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg
>> Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: +
>> 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360
>>
>> Email: m.end...@german-seed-alliance.de
>>
>> Firmensitz Köln Amtsgericht Köln, HRB 73844
>>
>> -Ursprüngliche Nachricht- Von: galaxy-dev
>> [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von
>> galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Donnerstag, 21.
>> Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff:
>> galaxy-dev Digest, Vol 138, Issue 9
>>
>> Send galaxy-dev mailing list submissions to
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>>
>> Today's Topics:
>>
>> 1. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)
>>
>>
>> --
>>
>>  Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo
>> <luop0...@gmail.com> To: Hans-Rudolf Hotz <h...@fmi.ch> Cc: galaxy-dev
>> <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Galaxy
>> v17.09 impersonation doesn't work Message-ID:
>> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ad...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hans-Rudolf,
>>
>> I just started a brand new galaxy with the default internal database.
>> I did the minimal change to galaxy.ini so that I could use CAS
>> authentication. Still, impersonation failed.
>>
>>
>> Ping
>>
>> On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <h...@fmi.ch>
>> wrote:
>>
>>> Hi Ping
>>>
>>>
>>> Does it work with a fresh installation ( v17.09) staring with an
>>> empty PostgrSQL database?
>>>
>>>
>>> Hans-Rudolf
>>>
>>> On 12/19/2017 03:41 PM, Ping Luo wrote:
>>>
>>>> Hans

Re: [galaxy-dev] MACS2 Error

2017-10-18 Thread Devon Ryan 

That doesn't change anything, I also using Galaxy within docker.


On 10/18/2017 06:27 PM, Deepak Tanwar wrote:

I am using Galaxy via Docker.

On Oct 18, 2017, at 11:51 AM, Devon Ryan <dprya...@gmail.com 
<mailto:dprya...@gmail.com>> wrote:


Assuming you don't have galaxy set to clean up job working 
directories upon failure, have a look at the tool_script.sh in that 
directory and see if you can discern the issue. Also check the conda 
activation log file (under working/ I think) in that directory to see 
if it has anything useful.


Devon


On 10/18/2017 05:46 PM, Deepak Tanwar wrote:

Hello,

I am still facing problem. I have tried to reinstall MACS2 but 
nothing helped.


Thank you!
Deepak


On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktan...@hotmail.com 
<mailto:dktan...@hotmail.com>> wrote:


Hi all,

There is some problem with MACS2:

export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: 
line 25: macs2: command not found Fatal error: Exit code 127 ()
Tool installed: 
/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 
<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>


Dependency Resolver Details
Dependency 	Version 	Resolver 	Exact version 	Current Installation 
Status 	

macs2   2.1.1.20160309  Conda   True
gawk4.1.3   Conda   True



Thank you,
Deepak




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--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email:dprya...@gmail.com




--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com

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Re: [galaxy-dev] MACS2 Error

2017-10-18 Thread Devon Ryan 
Assuming you don't have galaxy set to clean up job working directories 
upon failure, have a look at the tool_script.sh in that directory and 
see if you can discern the issue. Also check the conda activation log 
file (under working/ I think) in that directory to see if it has 
anything useful.


Devon


On 10/18/2017 05:46 PM, Deepak Tanwar wrote:

Hello,

I am still facing problem. I have tried to reinstall MACS2 but nothing 
helped.


Thank you!
Deepak


On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktan...@hotmail.com 
<mailto:dktan...@hotmail.com>> wrote:


Hi all,

There is some problem with MACS2:

export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: 
line 25: macs2: command not found Fatal error: Exit code 127 ()
Tool installed: 
/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 
<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>


Dependency Resolver Details
Dependency 	Version 	Resolver 	Exact version 	Current Installation 
Status 	

macs2   2.1.1.20160309  Conda   True
gawk4.1.3   Conda   True



Thank you,
Deepak




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--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com

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Re: [galaxy-dev] Job output not returned from Cluster Error

2017-08-17 Thread Devon Ryan 
Presuming SGE runs this on a remote node, it's likely the file hasn't been 
flushed to disk. Have you checked to see if the files eventually show up?

Sent from my iPhone

> On 17. Aug 2017, at 17:49, Yip, Miu ki  wrote:
> 
> Hi,
> 
> We’re having a bit of an error where the GUI shows that a job had an error. 
> When the user submits the job, the job is seen to have run via terminal and 
> uge. The job working directory exists and the out and error file is in there. 
> Once the job completes, it seems like the GUI will say that it works. But 
> then several minutes later, the GUI shows the job turning from green to red 
> and giving the error that the “Job output not returned from the Cluster” 
> error. 
> 
> I tried setting the retry_job_output_collection but it did not work (we’re 
> using a local file system): 
> http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-failed-quot-td4627406.html#a4632168
> 
> This seems to happen randomly for different jobs. Some jobs receive errors 
> but others do not receive this error. 
> 
> Does anybody have any suggestions on how to fix this? There is no error that 
> appears in the paster.log file and we are using SGE. 
> 
> Thanks in advance!
> ___
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Re: [galaxy-dev] Creating a tool dependency packages

2017-07-24 Thread Devon Ryan 
In general, see if the new package is available in conda-forge or
bioconda. If so, you just need to mention it in the requirements
section of the tool XML.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Mon, Jul 24, 2017 at 12:21 PM, Delisle Lucille
<lucille.deli...@epfl.ch> wrote:
> Hello Devon,
> Thank you very much for your quick answer. In fact in my 
> tool_dependencies.xml I did not put the '#':
> sha256sum="6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705">
>  
> https://pypi.python.org/packages/31/43/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz
>
> The log has been sent in a different e-mail (sorry).
>
> I think the conda is a really good alternative but I did not know how to ask 
> conda to resolve it.
> In fact, I need numexpr to install another python library and I do not know 
> how to write in this new package how to look for numexpr with conda.
>
> Thanks again,
>
> Lucille
>
> Lucille Delisle, PhD
> PostDoc Duboule Lab
> Laboratory of Developmental Genomics
> EPFL SV ISREC UPDUB
> SV 2843
> Station 19
> CH-1015 Lausanne
> Tel : +41 21 693 97 08
>
> ____
> De : dprya...@gmail.com <dprya...@gmail.com> de la part de Devon Ryan 
> <dpr...@dpryan.com>
> Envoyé : lundi 24 juillet 2017 12:06
> À : Delisle Lucille
> Cc : galaxy-dev@lists.galaxyproject.org
> Objet : Re: [galaxy-dev] Creating a tool dependency packages
>
> You can remove everything starting with the "#" in the URL, though I
> presume that's not the problem. Have a look in the installation log on
> your machine, perhaps there's an error message somewhere in it.
>
> More conveniently, though, numexpr-2.6.2 is available in conda-forge,
> so if you use conda as a dependency resolver then you can skip
> creating a tool dependency package. This saves a LOT of hassle, in my
> experience.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Mon, Jul 24, 2017 at 11:58 AM, Delisle Lucille
> <lucille.deli...@epfl.ch> wrote:
>> Dear Galaxy list,
>>
>>
>> I do not know if it is the right place to ask my question. I would like to
>> create a tool dependency package for numexpr (a python library).
>>
>> I tried to do it taking examples from different tool dependency packages
>> from iuc for example.
>>
>> I added my repository to the testtoolshed but when I tried to install it.
>> The directory lib/python of my tool is empty.
>>
>> My repository is : package_python_2_7_numexpr_2_6_2
>>
>> The big difference I see between the one from iuc and mine is the url:
>>
>> For example, for pybigwig, the URL is :
>> https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz
>>
>> For my library numexpr I could not find such a url so I put the one I
>> thought would be the good one:
>>
>> https://pypi.python.org/packages/31/43/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c
>>
>>
>> Thank you very much for your help,
>>
>>
>>
>> Lucille Delisle, PhD
>> PostDoc Duboule Lab
>> Laboratory of Developmental Genomics
>> EPFL SV ISREC UPDUB
>> SV 2843
>> Station 19
>> CH-1015 Lausanne
>> Tel : +41 21 693 97 08
>>
>> ___
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Re: [galaxy-dev] Creating a tool dependency packages

2017-07-24 Thread Devon Ryan 
You can remove everything starting with the "#" in the URL, though I
presume that's not the problem. Have a look in the installation log on
your machine, perhaps there's an error message somewhere in it.

More conveniently, though, numexpr-2.6.2 is available in conda-forge,
so if you use conda as a dependency resolver then you can skip
creating a tool dependency package. This saves a LOT of hassle, in my
experience.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Mon, Jul 24, 2017 at 11:58 AM, Delisle Lucille
<lucille.deli...@epfl.ch> wrote:
> Dear Galaxy list,
>
>
> I do not know if it is the right place to ask my question. I would like to
> create a tool dependency package for numexpr (a python library).
>
> I tried to do it taking examples from different tool dependency packages
> from iuc for example.
>
> I added my repository to the testtoolshed but when I tried to install it.
> The directory lib/python of my tool is empty.
>
> My repository is : package_python_2_7_numexpr_2_6_2
>
> The big difference I see between the one from iuc and mine is the url:
>
> For example, for pybigwig, the URL is :
> https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz
>
> For my library numexpr I could not find such a url so I put the one I
> thought would be the good one:
>
> https://pypi.python.org/packages/31/43/ab9535c416faabd1865453389260fdad0a23a714609c13112885009a/numexpr-2.6.2.tar.gz#md5=943f8e4be7569b1ad01b10cbaa002a5c
>
>
> Thank you very much for your help,
>
>
>
> Lucille Delisle, PhD
> PostDoc Duboule Lab
> Laboratory of Developmental Genomics
> EPFL SV ISREC UPDUB
> SV 2843
> Station 19
> CH-1015 Lausanne
> Tel : +41 21 693 97 08
>
> ___
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> in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Moving Shared Data Library Folders

2017-07-06 Thread Devon Ryan 
You end up needing to update the database, or at least I did a year or
two ago when I last did something like this. Thankfully, if you moved
things in a mostly predictable way you can do it with a bit of python
(the path is stored in the "external_filename" field of the "dataset"
table).

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Jul 6, 2017 at 8:30 AM, D K <danielforti...@gmail.com> wrote:
> Is it possible to move the file locations of Shared data libraries that have
> already been added to the system? I just tried moving some of these files to
> a new location (e.g. /somewhere/files to /somewhere_else/libraries) and
> updating the galaxy.ini entry to point to the new location. However, files
> previously added to a library still point to the old location.
> I found this question on biostars:
> https://biostar.usegalaxy.org/p/1119/
> Is the only way to do this sort of update to manually change such entries in
> the database?
>
> Thanks!
>
>
> ___
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Re: [galaxy-dev] DeepTools python dependency issues?

2017-07-05 Thread Devon Ryan 
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: dpr...@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.prev...@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 
> 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 
> 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 
> 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 
> 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 
> 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.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
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> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender
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> untersagt.
>
>
>
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Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
This is likely an issue with using active vs. passive FTP. Unfortunately
since you're not using `--net=host` you can't use passive ftp (at least
it's never worked for me). Perhaps sftp on port 8022 will work better.

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
<devon.r...@dzne.de>

On Fri, Jun 23, 2017 at 1:06 PM, Md. Rezaul Karim <
rezaul.ka...@insight-centre.org> wrote:

> Timeout detected. (data connection)
> Could not retrieve directory listing
> Error listing directory '/'.
>
>
> However, when I tried from Ubuntu terminal it gets connected. However, I
> am getting below error:
>
> asif@ubuntu:~$ ftp 10.196.106.60 8021
> Connected to 10.196.106.60.
> 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [:::172.17.0.2]
> Name (10.196.106.60:asif): rezaul.ka...@insight-centre.org
> 331 Password required for rezaul.ka...@insight-centre.org
> Password:
> 230 User rezaul.ka...@insight-centre.org logged in
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> ls
> 500 Illegal PORT command
> ftp: bind: Address already in use
> ftp> quit
> 221 Goodbye.
>
>
> Regards,
> _
> *Md. Rezaul Karim*, BSc, MSc
> Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
> <http://139.59.184.114/index.html>
>
> On 23 June 2017 at 12:01, Devon Ryan <dpr...@dpryan.com> wrote:
>
>> Do you get an error of some sort?
>>
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@dpryan.com
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>> <devon.r...@dzne.de>
>>
>> On Fri, Jun 23, 2017 at 12:33 PM, Md. Rezaul Karim <
>> rezaul.ka...@insight-centre.org> wrote:
>>
>>> Hi Devon,
>>>
>>> I tried to connect to Galaxy instance with FTP client WinSCP as follows:
>>>
>>> [image: Inline images 1]
>>>
>>> But no luck. Even I tried with the DNS (i.e.
>>> http://bioopenergalaxy.insight-centre.org/) and changing SFTP to FTP
>>> and tried with port number 21 and 8021 too.
>>>
>>>
>>>
>>>
>>> Regards,
>>> _
>>> *Md. Rezaul Karim*, BSc, MSc
>>> Researcher, INSIGHT Centre for Data Analytics
>>> National University of Ireland, Galway
>>> IDA Business Park, Dangan, Galway, Ireland
>>> Web: http://www.reza-analytics.eu/index.html
>>> <http://139.59.184.114/index.html>
>>>
>>> On 23 June 2017 at 11:05, Md. Rezaul Karim <
>>> rezaul.ka...@insight-centre.org> wrote:
>>>
>>>> Ok, thanks for the clarification. I will try again and get back to you.
>>>>
>>>>
>>>>
>>>> On Jun 23, 2017 11:03 AM, "Devon Ryan" <dpr...@dpryan.com> wrote:
>>>>
>>>>> If your user is an admin then yes. Each user can use their normal
>>>>> login credentials.
>>>>> --
>>>>> Devon Ryan, Ph.D.
>>>>> Email: dpr...@dpryan.com
>>>>> Data Manager/Bioinformatician
>>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>>> Stübeweg 51
>>>>> 79108 Freiburg
>>>>> Germany
>>>>>
>>>>>
>>>>> On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim
>>>>> <rezaul.ka...@insight-centre.org> wrote:
>>>>> > Did you mean using the admin user email id and the password?
>>>>> >
>>>>> > Regards,
>>>>> > _
>>>>> > Md. Rezaul Karim, BSc, MSc
>>>>> > Researcher, INSIGHT Centre for Data Analytics
>>>>> > National University of Ireland, Galway
>>>>> > IDA Business Park, Dangan, Galway, Ireland
>>>>> > Web: http://www.reza-analytics.eu/index.html
>>>>> >
>>>>> > On 23 June 2017 at 10:44, Devon Ryan <dpr...@dpryan.com> wrote:
>>>>> >>
>>>>> >> You should be able to login with the email address and password that
>>>>> >> you use for Galaxy then. That works for my instances at least.
>>>>> >> --
>>>>>

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
If your user is an admin then yes. Each user can use their normal
login credentials.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim
<rezaul.ka...@insight-centre.org> wrote:
> Did you mean using the admin user email id and the password?
>
> Regards,
> _
> Md. Rezaul Karim, BSc, MSc
> Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
>
> On 23 June 2017 at 10:44, Devon Ryan <dpr...@dpryan.com> wrote:
>>
>> You should be able to login with the email address and password that
>> you use for Galaxy then. That works for my instances at least.
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@dpryan.com
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>> On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim
>> <rezaul.ka...@insight-centre.org> wrote:
>> > Hi Devon,
>> >
>> > Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy
>> > is
>> > built on top of it (version 17.05). My system admin has provided me with
>> > the
>> > IP address of this DNS and when I issue the FTP command as follows:
>> >
>> > asif@ubuntu:~$ ftp 10.196.106.60 8021
>> >
>> > It shows:
>> >
>> > Connected to 10.196.106.60.
>> > 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [:::172.17.0.2]
>> > Name (10.196.106.60:asif):
>> >
>> > It seems ProFTPD is already configured. While running the container,
>> > port
>> > 8021 was mapped to 21.
>> >
>> >
>> > Regards,
>> > _
>> > Md. Rezaul Karim, BSc, MSc
>> > Researcher, INSIGHT Centre for Data Analytics
>> > National University of Ireland, Galway
>> > IDA Business Park, Dangan, Galway, Ireland
>> > Web: http://www.reza-analytics.eu/index.html
>> >
>> > On 23 June 2017 at 10:30, Devon Ryan <dpr...@dpryan.com> wrote:
>> >>
>> >> Are you using galaxy-docker-stable from Björn
>> >> (https://github.com/bgruening/docker-galaxy-stable) or did you make
>> >> your own dockerized-Galaxy version? Björn's runs proFTPd by default,
>> >> so if you're using it then ensure that's running in the container.
>> >>
>> >> Devon
>> >> --
>> >> Devon Ryan, Ph.D.
>> >> Email: dpr...@dpryan.com
>> >> Data Manager/Bioinformatician
>> >> Max Planck Institute of Immunobiology and Epigenetics
>> >> Stübeweg 51
>> >> 79108 Freiburg
>> >> Germany
>> >>
>> >>
>> >> On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim
>> >> <rezaul.ka...@insight-centre.org> wrote:
>> >> > Dear All,
>> >> >
>> >> > I have Dockerized the Galaxy and it's running as a containerized
>> >> > application
>> >> > on the DC/OS server. It can be accessed at
>> >> > http://bioopenergalaxy.insight-centre.org/.
>> >> >
>> >> > However, I'm wondering how to FTP files on it. Please note that I
>> >> > have
>> >> > the
>> >> > following configuration on the galaxy.ini file:
>> >> >
>> >> > # This should point to a directory containing subdirectories matching
>> >> > users'
>> >> > identifier (defaults to e-mail), where Galaxy will look for files.
>> >> > ftp_upload_dir = /export/ftp
>> >> >
>> >> > # This should be the hostname of your FTP server, which will be
>> >> > provided
>> >> > to
>> >> > users in the help text.
>> >> > ftp_upload_site = bioopenergalaxy.insight-centre.org
>> >> >
>> >> >
>> >> > Any help or pointer would be highly appreciated.
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > Regards,
>> >> > _
>> >> > Md. Rezaul Karim, BSc, MSc
>> >> > Researcher, INSIGHT Centre for Data Analytics
>> >> > National University of Ireland, Galway
>> >> > IDA Business Park, Dangan, Galway, Ireland
>> >> > Web: http://www.reza-analytics.eu/index.html
>> >> >
>> >> > ___
>> >> > 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/
>> >
>> >
>
>
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Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
You should be able to login with the email address and password that
you use for Galaxy then. That works for my instances at least.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim
<rezaul.ka...@insight-centre.org> wrote:
> Hi Devon,
>
> Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy is
> built on top of it (version 17.05). My system admin has provided me with the
> IP address of this DNS and when I issue the FTP command as follows:
>
> asif@ubuntu:~$ ftp 10.196.106.60 8021
>
> It shows:
>
> Connected to 10.196.106.60.
> 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [:::172.17.0.2]
> Name (10.196.106.60:asif):
>
> It seems ProFTPD is already configured. While running the container, port
> 8021 was mapped to 21.
>
>
> Regards,
> _
> Md. Rezaul Karim, BSc, MSc
> Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
>
> On 23 June 2017 at 10:30, Devon Ryan <dpr...@dpryan.com> wrote:
>>
>> Are you using galaxy-docker-stable from Björn
>> (https://github.com/bgruening/docker-galaxy-stable) or did you make
>> your own dockerized-Galaxy version? Björn's runs proFTPd by default,
>> so if you're using it then ensure that's running in the container.
>>
>> Devon
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@dpryan.com
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>> On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim
>> <rezaul.ka...@insight-centre.org> wrote:
>> > Dear All,
>> >
>> > I have Dockerized the Galaxy and it's running as a containerized
>> > application
>> > on the DC/OS server. It can be accessed at
>> > http://bioopenergalaxy.insight-centre.org/.
>> >
>> > However, I'm wondering how to FTP files on it. Please note that I have
>> > the
>> > following configuration on the galaxy.ini file:
>> >
>> > # This should point to a directory containing subdirectories matching
>> > users'
>> > identifier (defaults to e-mail), where Galaxy will look for files.
>> > ftp_upload_dir = /export/ftp
>> >
>> > # This should be the hostname of your FTP server, which will be provided
>> > to
>> > users in the help text.
>> > ftp_upload_site = bioopenergalaxy.insight-centre.org
>> >
>> >
>> > Any help or pointer would be highly appreciated.
>> >
>> >
>> >
>> >
>> > Regards,
>> > _
>> > Md. Rezaul Karim, BSc, MSc
>> > Researcher, INSIGHT Centre for Data Analytics
>> > National University of Ireland, Galway
>> > IDA Business Park, Dangan, Galway, Ireland
>> > Web: http://www.reza-analytics.eu/index.html
>> >
>> > ___
>> > 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/
>
>
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Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
Are you using galaxy-docker-stable from Björn
(https://github.com/bgruening/docker-galaxy-stable) or did you make
your own dockerized-Galaxy version? Björn's runs proFTPd by default,
so if you're using it then ensure that's running in the container.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim
<rezaul.ka...@insight-centre.org> wrote:
> Dear All,
>
> I have Dockerized the Galaxy and it's running as a containerized application
> on the DC/OS server. It can be accessed at
> http://bioopenergalaxy.insight-centre.org/.
>
> However, I'm wondering how to FTP files on it. Please note that I have the
> following configuration on the galaxy.ini file:
>
> # This should point to a directory containing subdirectories matching users'
> identifier (defaults to e-mail), where Galaxy will look for files.
> ftp_upload_dir = /export/ftp
>
> # This should be the hostname of your FTP server, which will be provided to
> users in the help text.
> ftp_upload_site = bioopenergalaxy.insight-centre.org
>
>
> Any help or pointer would be highly appreciated.
>
>
>
>
> Regards,
> _
> Md. Rezaul Karim, BSc, MSc
> Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
>
> ___
> 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/
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[galaxy-dev] "Execute" button does nothing in the CrossMap tool?

2017-04-03 Thread Devon Ryan 
Hi everyone,

I'm observing a very odd problem that presumably has something to do
with upgrading to Galaxy 17.01 on Friday. Since then, the "Execute"
button on the CrossMap tools (from yhoogstrate) does nothing. Upon
checking the server logs and the firefox console it looks like there's
not even a request sent to Galaxy when a user clicks on the "Execute"
button. I recall that the tools worked before, so I can only presume
that this is related to the upgrade to 17.01. Has anyone observed
anything similar or have suggestions regarding where to start
debugging this? I'll note that the user that reported this has tried
multiple browsers (firefox and safari) with the same result (nothing
happening) in both.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
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Re: [galaxy-dev] DeepTools installation error

2017-03-08 Thread Devon Ryan 
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" <dprya...@gmail.com 
<mailto:dprya...@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

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-- 
Devon Ryan, PhD

Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email:dprya...@gmail.com <mailto:dprya...@gmail.com>

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Email: dprya...@gmail.com
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Re: [galaxy-dev] DeepTools installation error

2017-03-08 Thread Devon Ryan 

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



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Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com

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Re: [galaxy-dev] Shared Data Library, large number of files

2017-03-02 Thread Devon Ryan 
I observe the same thing on 16.07. As an example, I'm just opened a
data library under Admin->Data->Data Libraries and this took about a
minute and a half. It looks like this is related to the quantity of
data in this folder. The associated entry in the uwsgi log is as
follows:

[pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
[Thu Mar  2 08:40:19 2017] GET
/library_common/browse_library?sort=name=All=All=False=library_admin=browse=355326571f7132ff
=> generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
in 73 bytes (14 switches on core 2)

So this library is causing ~21 megs of data to be returned to the
browser, which I presume is the source of the issue.

As an aside, the old data library API is still in use in the admin
section until at least 16.07. Perhaps this has been changed since
then, I hadn't planed to update our system until the end of the month.
For what it's worth, opening the same library via "shared data" takes
~100 msec.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Thu, Mar 2, 2017 at 8:30 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
> this sounds more like a browser issue to me
> which browser do you use? what happens when you use a different browser? and
> what happens when you just reload the page
>
>
> Hans-Rudolf
>
> On 03/01/2017 06:17 PM, D K wrote:
>>
>> Actually, when I click on the Shared Data-> Data Libraries link I get
>> only the Galaxy banner and a blank page, so I'm not even seeing the data
>> libraries themselves.
>>
>> If I use the Admin link and then click Data libraries, I can see the
>> actual libraries. But when I try to enter one of the libraries with lots
>> of files it hangs.
>>
>>
>> On Wed, Mar 1, 2017 at 9:03 AM, D K <danielforti...@gmail.com
>> <mailto:danielforti...@gmail.com>> wrote:
>>
>> Hi Hans,
>>
>> I'm running 16.10. If I'm not mistaken, the old Data Library
>> interface is still accessible in the Admin menu isn't it? I have the
>> same issue when navigating to a Data Library either from the Admin
>> or Shared Data links. I also tried this in 16.07 with the same
>> result.  If it makes a difference, I'm using PostgreSQL and Apache.
>>
>> Dwight
>>
>>
>>
>> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <h...@fmi.ch
>> <mailto:h...@fmi.ch>> wrote:
>>
>> Hi Daniel
>>
>> Just double checking which version of galaxy are you running? In
>> other words: are you still using the old Data Library interface?
>> (if I remember correctly, the old UI was deprecated in 15.10)
>> We had similar issues with the old UI.
>>
>> The new one works fine and is very fast. E.g. we have a 'MISEQ'
>> folder with more than 100 sub folders and a HISEQ folder with
>> more than 600 sub folders. Each containing up to 100plus fastq
>> and text files.
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>> On 03/01/2017 12:13 AM, D K wrote:
>>
>> Hi,
>>
>> I've noticed that the more files / folders (think hundreds
>> of folders
>> each with 20+ fastq files) I add to a Shared Data Library,
>> the longer
>> and longer it takes to initially navigate the folder
>> structure (after
>> clicking on the specific Shared Data Library). Just opening
>> up the
>> Shared Data Library can take several minutes and often the
>> browser times
>> out. Is there a way to speed this up?
>>
>> If it's relevant, when I add shared data, it's linked rather
>> than copied
>> into Galaxy. Any suggestions would be greatly appreciated
>>
>> Thanks!
>>
>>
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Re: [galaxy-dev] wrapper for tool with multiple outputs

2017-01-04 Thread Devon Ryan 
Hi Jochen,

Don't have it use /tmp, but rather the current working directory and
then everything will work. Galaxy jobs are run in individual working
directories, so you can exploit that to ensure that files aren't
overwritten.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, Jan 4, 2017 at 12:32 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
> Hi,
>
> I have a tool that produces multiple output files a log file, two bam files.
> (https://github.com/nugentechnologies/nudup)
>
> The tool it self provides an option called --out to specify a path to a
> directory with a prefix that will be added to the output files:
>
> --out /tmp/out
>
> this will produce 3 files:
>
> /tmp/out_dup_log.txt
> /tmp/out.sorted.dedup.bam
> /tmp/out.sorted.markdup.bam
>
> so my question is if this out prefix will give me problems overwriting next
> output files coming from this tool?
>
>
> Cheers Jochen
>
>
>
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Re: [galaxy-dev] building indexes

2016-10-03 Thread Devon Ryan 

Have you tried the bwtsw method in the bwa mem data manager?

Regarding the 2bit file, even if you make it, are you sure the 
downstream tool(s) will handle the missing chromosomes/contigs?


Maybe you should use the primary assembly instead (at least for the 2bit 
file).


Devon

On 10/03/2016 03:50 PM, Nikolaos Tur wrote:

Hi,

I try to build indexes for ch38 (GRCh38.84 Toplevel) using data 
managers for BWA-MEM and TwoBit.

Both failed.

Error building index:
Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit 
format does not support indexes larger than 4Gb,

please split up into smaller files.

[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 
46629609168 bytes at bwtindex.c line 135: Cannot allocate memory

Error building index.

So, how to split genome for TwoBit and how much RAM is needed for BWA 
indexes? These errors are from runs on machine with 45GB RAM.


Thanx,
Nikolaos


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--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com

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Re: [galaxy-dev] Parameters out

2016-08-30 Thread Devon Ryan 
Hi Katherine,

That one's beyond me, sorry.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Tue, Aug 30, 2016 at 2:46 PM, Katherine Beaulieu
<katherine.beaulieu...@gmail.com> wrote:
> Hi Devon,
> Thanks for the information! Do you know where in the code base Galaxy
> accesses these values for tool execution though?
> Cheers,
> Katherine
>
> On Tue, Aug 30, 2016 at 8:44 AM, Devon Ryan <dpr...@dpryan.com> wrote:
>>
>> Hi Katherine,
>>
>> Check the 'job_parameter' table, though you'll need to find the
>> correct job ID from the 'job' table.
>>
>> Devon
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@dpryan.com
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>> On Tue, Aug 30, 2016 at 2:35 PM, Katherine Beaulieu
>> <katherine.beaulieu...@gmail.com> wrote:
>> > Hi everyone,
>> > Does anyone know where parameters are being retrieved from the database
>> > during tool execution within Galaxy's files. I am trying to change a
>> > value
>> > in the database after the value has been retrieved.
>> > Thanks!
>> > Katherine
>> >
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>
>
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Re: [galaxy-dev] Parameters out

2016-08-30 Thread Devon Ryan 
Hi Katherine,

Check the 'job_parameter' table, though you'll need to find the
correct job ID from the 'job' table.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Tue, Aug 30, 2016 at 2:35 PM, Katherine Beaulieu
<katherine.beaulieu...@gmail.com> wrote:
> Hi everyone,
> Does anyone know where parameters are being retrieved from the database
> during tool execution within Galaxy's files. I am trying to change a value
> in the database after the value has been retrieved.
> Thanks!
> Katherine
>
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