[galaxy-dev] BLAST only using single core
Previously, the BLAST wrapper was able to use multiple cores but recently users have started complaining it has got really slow and when I look at the cluster a job is only using a single core. I don’t want jobs split across multiple cluster nodes, but each node has 16 cores so it would be good if they could be used. I’m still using the older 16.01 release and this has been upgraded repeatedly over the last few years so I’m still using the universe_wsg.ini file (sym linked to config/galaxy.ini) and I don’t have a job_conf.xml set up. I’m using drmaa to drive an LSF cluster. BLAST is the main issue here so I was wondering if there’s a way to pass the -num_threads flag without breaking everything until I can build up a new server? Dr. Shane Sturrock NZGL BioIT Admin n...@biomatters.com ___ 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/mailinglists/
Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not in Toolshed
Hi, > Hello Bjoern, > > Thanks for the quick response, I appreciate that. > > Concerning the instructions, I am unclear of a couple of things. > > I have a folder with my tools, there is no preinstalled folder that > these tools need to go in called my_tools_folder, right? No, you can create such a folder wherever you want and name it like you want :) > Additionally, would I place this tool in the same directory level as > Galaxy_Central or as the config directory? (My current set up is > galaxy_storage -> galaxy-central -> config, I have my tools folder in > the same level as galaxy-central.) This does not matter, what matters is that the folder path is correct in the env variable. > Lastly, the environment variable, is there a specific file that all > the environment variables are stored for docker Galaxy? I have tried > looking for an env file, but could not find it. There is no file. These are real environment variables that are created by Docker during container start. You can change them during start with (e.g): docker run -e MY_ENV_VAR=foo bgruening/galaxy-stable If such a variable, beginning with GALAXY_CONFIG_XXX exists this will be picked up by Galaxy. Have a look at the container there are a lot GALAXY_CONFIG_ vars set. Hope this helps, Bjoern > Thanks so much! Miuki From: > Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, July 20, > 2016 2:23 AM To: Yip, Miu ki; galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installing > tools not in Toolshed > > Hi Miuki! > > Am 19.07.2016 um 22:36 schrieb Yip, Miu ki: >> Hello Galaxy Team, >> >> We're from the Bioinformatics Shared Resources at Cold Spring >> Harbor Lab and we're trying to create a new flavour of Galaxy for >> local use in the lab using docker containers. >> >> We want to add tools that are specific for our lab, such as >> importing files from our system, onto this flavour of Galaxy using >> Docker containers. Is there a recommended way to do this? > > Can you try the following, assuming that all your tools are in > my_tools_tolder. > > ADD ./my_tools_folder /inhouse_tools/ > > Now we need a tool_conf.xml file. You can create an additional one, > no need to modify the existing one. I would propose to include this > config file also in ./my_tools_folder so it will end up in > /inhouse_tools/tool_conf.xml With the following environment variable > you tell Galaxy about the additional tool_conf file. > > ENV GALAXY_CONFIG_TOOL_CONFIG_FILE = > config/tool_conf.xml,config/shed_tool_conf.xml,/inhouse_tools/tool_conf.xml > > Please make sure that your new tools in > /inhouse_tools/tool_conf.xml have as path "/inhouse_tools/.xml". > > Let me know if this works, we should add this to the readme. > > Thanks, Bjoern > >> I've taken a look at the README from: >> https://github.com/bgruening/docker-galaxy-stable >> >> I have been able to successfully create an instance of Galaxy >> where the homepage is different and tools are imported from the >> Tool Shed. However, I cannot figure out how to install tools onto >> Galaxy that are not from the Tool Shed. I have tried creating a >> container, putting the tools into the tools folder, changing the >> tool conf and the integrated tool panel xml file. Then committing >> the container and creating a new image. From the new image, I tried >> creating another container and running it. This does not create a >> Galaxy instance with the new tool. (This also does not seem like >> the best way to go about something like this.) > > >> Thank you for your help. >> >> Best, Miuki Yip >> ___ 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/mailinglists/ >> ___ 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/mailinglists/
Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not in Toolshed
Hello Bjoern, Thanks for the quick response, I appreciate that. Concerning the instructions, I am unclear of a couple of things. I have a folder with my tools, there is no preinstalled folder that these tools need to go in called my_tools_folder, right? Additionally, would I place this tool in the same directory level as Galaxy_Central or as the config directory? (My current set up is galaxy_storage -> galaxy-central -> config, I have my tools folder in the same level as galaxy-central.) Lastly, the environment variable, is there a specific file that all the environment variables are stored for docker Galaxy? I have tried looking for an env file, but could not find it. Thanks so much! Miuki From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, July 20, 2016 2:23 AM To: Yip, Miu ki; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not in Toolshed Hi Miuki! Am 19.07.2016 um 22:36 schrieb Yip, Miu ki: > Hello Galaxy Team, > > We're from the Bioinformatics Shared Resources at Cold Spring Harbor > Lab and we're trying to create a new flavour of Galaxy for local use > in the lab using docker containers. > > We want to add tools that are specific for our lab, such as importing > files from our system, onto this flavour of Galaxy using Docker > containers. Is there a recommended way to do this? Can you try the following, assuming that all your tools are in my_tools_tolder. ADD ./my_tools_folder /inhouse_tools/ Now we need a tool_conf.xml file. You can create an additional one, no need to modify the existing one. I would propose to include this config file also in ./my_tools_folder so it will end up in /inhouse_tools/tool_conf.xml With the following environment variable you tell Galaxy about the additional tool_conf file. ENV GALAXY_CONFIG_TOOL_CONFIG_FILE = config/tool_conf.xml,config/shed_tool_conf.xml,/inhouse_tools/tool_conf.xml Please make sure that your new tools in /inhouse_tools/tool_conf.xml have as path "/inhouse_tools/.xml". Let me know if this works, we should add this to the readme. Thanks, Bjoern > I've taken a look at the README from: > https://github.com/bgruening/docker-galaxy-stable > > I have been able to successfully create an instance of Galaxy where > the homepage is different and tools are imported from the Tool Shed. > However, I cannot figure out how to install tools onto Galaxy that > are not from the Tool Shed. I have tried creating a container, > putting the tools into the tools folder, changing the tool conf and > the integrated tool panel xml file. Then committing the container and > creating a new image. From the new image, I tried creating another > container and running it. This does not create a Galaxy instance with > the new tool. (This also does not seem like the best way to go about > something like this.) > Thank you for your help. > > Best, Miuki Yip > ___ 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/mailinglists/ > ___ 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/mailinglists/
Re: [galaxy-dev] Fwd: New galaxy parameter type
Dear all,
I did not want to open a new subject, because I have the same problem.
I tried to follow what is was described here
https://github.com/galaxyproject/galaxy/pull/393, I add the lines a
described in the github, but when I am clicking to my tool I got
[image: Images intégrées 1]
And if i check the error in commad line I have
galaxy.web.framework.decorators ERROR 2016-07-20 10:05:44,357 Uncaught
exception in exposed API method:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 258, in decorator
rval = func( self, trans, *args, **kwargs)
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
line 100, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2383,
in to_json
populate_state(trans, self.inputs, state_inputs, state_errors,
params.__dict__)
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2255,
in populate_state
state[input.name] = input.get_initial_value(trans, context,
history=history)
TypeError: get_initial_value() got an unexpected keyword argument 'history'
10.38.149.37 - - [20/Jul/2016:10:05:44 +0200] "GET
/api/tools/irods_pull_main/build HTTP/1.1" 500 - "http://10.38.152.152:8080/;
"Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/51.0.2704.103 Safari/537.36"
Maybe something to add for the new version of galaxy ?
Thanks in advance,
Mohamed
2016-07-15 21:54 GMT+02:00 Martin Čech :
> forwarding to the list
>
>
> -- Forwarded message -
> From: Katherine Beaulieu
> Date: Fri, Jul 15, 2016 at 3:45 PM
> Subject: Re: [galaxy-dev] New galaxy parameter type
> To: Martin Čech
>
>
> Thanks Peter, I will look into that. The reason I am asking is because of
> what Mohammed asked earlier as well. I developed two tools which allow you
> to import and export information from a program called irods but you need
> to be able to authenticate with irods to be able to do so. Thanks again for
> always being helpful!
>
> On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech wrote:
>
>> Katherine please disregard my answer, I probably misread your question. :)
>> M.
>>
>> On Fri, Jul 15, 2016 at 3:05 PM Peter Cock
>> wrote:
>>
>>> Did you mean parameter as in input field shown
>>> to the user? Like a combobox or text field?
>>>
>>> Since this happened to come up earlier today, here's
>>> a rejected pull request which added a password
>>> parameter - that ought to give you a rough idea:
>>>
>>> https://github.com/galaxyproject/galaxy/pull/393
>>>
>>> Peter
>>>
>>> On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu
>>> wrote:
>>> > Hi everyone,
>>> > I am looking to implement a new parameter type for galaxy tool
>>> development.
>>> > Does anyone know what would be involved in doing something like this or
>>> > perhaps what files would need to be edited?
>>> >
>>> >
>>> > ___
>>> > Please keep all replies on the list by using "reply all"
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>>> > 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/mailinglists/
>>> ___
>>> Please keep all replies on the list by using "reply all"
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>>> and other Galaxy lists, please use the interface at:
>>> https://lists.galaxyproject.org/
>>>
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>>> http://galaxyproject.org/search/mailinglists/
>>
>>
>
> ___
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> 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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>
___
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