July 2014 - galaxy-dev - lists.galaxyproject.org

adding javascript based tool in local instance of Galaxy
by Shyamasree Saha 14 Jul '14

14 Jul '14

Dear Galaxy Team, I want incorporate a genome browser into my my local instance of Galaxy. I have tried to view the html page that basically load all the javascripts associated with the browser and display the annotation. Even though it stopped complaining about java scripts in my html file after I have made sanitize_all_html= false, but it does not display anything. So, as next step i tried to take the path of visualization and add my tool as visualize plugin. I have again failed to do so. I followed the instruction given here https://wiki.galaxyproject.org/VisualizationsRegistry , and I am getting following error AttributeError: 'Bunch' object has no attribute 'template_lookup' URL: http://127.0.0.1:8080/visualization/show/Genoverse?dataset_id=2d9035b3fc152… File '/home/shyama/workspace/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/shyama/workspace/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/shyama/workspace/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py<http://httpexceptions.py/>', line 633 in __call__ return self.application(environ, start_response) File '/home/shyama/workspace/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/shyama/workspace/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/shyama/workspace/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/home/shyama/workspace/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/visualization.py', line 824 in render embedded=embedded, query=kwargs, vars={}, config=config, **resources ) File '/home/shyama/workspace/galaxy-dist/lib/galaxy/web/base/pluginframework.py', line 592 in fill_template return trans.fill_template( template_filename, template_lookup=plugin.template_lookup, **kwargs ) AttributeError: 'Bunch' object has no attribute 'template_lookup' I have even tried very simple thing, as mentioned in the tutorial, still getting this error. Can you kindly help me with this please? Many Thanks Shyama

2 1

Swiss-German Galaxy Tour: Sep 30th to Oct 2nd - Training day - Workshop - Developers day
by Hans-Rudolf Hotz 14 Jul '14

14 Jul '14

Dear all After the big success of the "Swiss Galaxy Workshop" two years ago, we are going to organize a similar event again in Bern on Wednesday October first. https://wiki.galaxyproject.org/Events/Switzerland2014 Like last time, the aim is to discuss the status of the Galaxy project, new developments, interface to other systems, extensions and best practice in reproducible research. We also welcome participants who are using workflow management systems other than Galaxy and tool developers who are looking for such systems to offer their tools to a wider audience. This year, the workshop will be part of a three day event (https://wiki.galaxyproject.org/Events/SG2014) - Prior to the workshop, we run a Galaxy training/demo Day on Tuesday September, 30th also in Bern (Switzerland) - Following the workshop, we organize a Developers Day on Thursday, October 2nd in Freiburg (Germany) The Developers Day is aimed at Galaxy hackers, tool and visualization developers. The format is still in discussion, but we intend to talk about: - defining tools and data sources to Galaxy - using Galaxy with different data stores (ObjectStore) - the Galaxy API Similar to the Workshop the day before, presentations by attendees of the Developers Day are highly encouraged. Titles can be submitted at registration time. Registration is free, but space is limited. We recommend you register soon to secure your spot on one, two or all three days of the SG2014Tour: http://www.surveymonkey.com/s/SG2014Tour Looking forward to see many of you in Bern and Freiburg Regards, Bjoern and Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

1 0

slurm drmaa and main galaxy
by Jillian Rowe 13 Jul '14

13 Jul '14

Hello, We are looking for a developer/admin/whoever consultant that can help us incorporated the slurm drmaa into galaxy. This is not a long term job, but a contracted and possible consultant job. Some requirements. 1. Must be compatible with the main galaxy. Changing some values in a config file is ok, but we don't want for it to break every time there is an update to galaxy. 2. We want to run jobs as the logged in user. 3. The developer must be familiar with git version control. We have a development and production instance of galaxy running. Best, Jillian

1 0

Clonable Galaxy installation
by Srinivas . 11 Jul '14

11 Jul '14

Hello, I am writing to inquire if there are considerations which would prevent creation of multiple instances of Galaxy by cloning a reference Galaxy installation containing a pre-configured set of tools and related assets. Both the reference and cloned instances would reside in the same cluster, and are each built within dedicated virtual machines . A Docker based approach has yet to be attempted but the same question likely applies. One issue that was observed in attempting this was that the Tool Shed populates the “shed_tool_data_table_conf.xml” file with absolute paths to the “.loc” files for tools installed via the Tool Shed (even though all path related variables are specified using relative paths in the respective configuration files). Might there be other similar dependencies or constraints, including those in the database, that would disallow this clonable Galaxy installation model from being viable ? With regard to the Tool Shed updating files with absolute paths: Could the Toolshed be configured to use relative paths ? Else, would it be OK to update the "file path" variables within the instances created from the reference installation to reflect the instance-specific file paths ? Thanks in advance. --Srinivas

2 3

Re: [galaxy-dev] removing wrapper version info from tools?
by Björn Grüning 11 Jul '14

11 Jul '14

Hi Nik, > Hi Bjorn, > > Thanks for your response. It seems to me that the wrapper version is not > really that useful... the thing that is important is the version of the > underlying tool. Sure, I agree. But on the other side the user should not care about the version, and is on most cases not interested as long as it works :) But as pointed out I would also like to shift to a more useful numbering, that the arbitrary one we are using now. I can certainly update the versions to be the versions of > the tool, if need be. That will break many thing, if you combining your tools with the toolshed and updates would be more complicated. Don't do that, at least not for tools from the ToolShed. Try to convince the Tool Maintainers. However, I wasn't aware that you could have multiple > versions of the same tool to choose from. How do I get that to work? You can simply install multiple versions (revisions) from the same tool from the Tool Shed. For example multimple Blast version. > I tried creating two different XML files with the same tool id, but that > didn't work. And how would I make sure the wrapper scripts pointed to the > correct version... it seems like I would have to tailor each script with an > absolute path to the specific version....? No you need to have the Tool Shed managing that for you. Each version is a separate tool with the same tool-id. Galaxy keeps track of every dependency of a certain tool. So the same tool with different versions with different dependencies will be working over time. Please read more about all of that in the galaxy wiki, especially about Tools and the Tool Shed: https://wiki.galaxyproject.org/ToolShed Cheers, Bjoern > - Nik. > > > On Mon, Jul 7, 2014 at 11:56 PM, Björn Grüning <bjoern.gruening(a)gmail.com> > wrote: > >> Hi Nik, >> >> you can hack to tool rendering and omit the version string, but I would >> not recommend that. The version will be a selectbox as soon as you have >> multiple versions from the same tools installed. This is important for >> reproducibility. >> The best approach would be to fix the version string. Do you have any >> suggestions? >> For my wrappers I try to go with that version scheme: >> {Tool-Version}.{wrapper-version}. >> >> Cheers, >> Bjoern >> >> Am 08.07.2014 08:51, schrieb Nikhil Joshi: >> >>> Hi all, >>> >>> So I am trying to remove the version info (at the top of a tool page) >>> entirely for all the tools. As I understand, those versions are the >>> versions of the wrappers and not the tools themselves. Although I could >>> change that, I would rather just not have the versions on the tool pages >>> at >>> all. We currently show all the versions of our tools on our landing page. >>> Is there any way to remove the version part of the tool title entirely? >>> I.e., if it originally says "Map with BWA for Illumina (version 1.0.0)", I >>> just want it to say "Map with BWA for Illumina". >>> >>> - Nik. >>> >>> >>> >>> ___________________________________________________________ >>> 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: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >>> > >

2 2

about parallel computing
by xunyao＠gmail.com 10 Jul '14

10 Jul '14

Dear Galaxy Team, Recently I and my colleges installed the Galaxy in our server,here I have several questions in using process. First is about the parallel computing, Galaxy itselef can process parallel computing by setting JobConfig, this is right? Second about the upload File Format, because our team intalled some new analysis functions to process the many '.CEL' in one folder based on the Galaxy, could you add ".CEL" upload? Or can direct upload .ZIP file? I see the explaination in the webpage: " You can also upload compressed files, which will automatically be decompressed", but when I upload a .ZIP file, Galaxy notices "ZIP file contained more than one file, only the first file was added to Galaxy." Could you add the function for uploading .ZIP file which contains some files? We plan to install some feature functions and workflows on Galaxy, and provide Chinese version analysis server based on Galaxy. Hope we can further collaborate in future. Looking forward to your reply. Bests, Mingzhu Zhu Assistant Researcher in Institute of Basic Medical Sciences Chinese Academy of Medical Sciences

1 0

Uploading files
by Matthew Birnie 09 Jul '14

09 Jul '14

Hi, I am having trouble uploading files. I have been attempting to upload four files since noon (GMT) yesterday however the problem shows that the files are still uploading. I have cancelled the operation a couple of times hours after starting the upload to try again but still nothing is happening. Is there an issue at the moment with uploading files? Kind regards, Matthew Birnie -- matthew.birnie(a)bristol.ac.uk Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology School of Clinical Sciences University of Bristol Dorothy Hodgkin Building Whitson Street Bristol BS1 3NY (T) 0117 331 3124

3 2

moving tool-data : no build genome retrieve
by julie dubois 09 Jul '14

09 Jul '14

Hi all, I'm moving the directory "tool-data" in other partition than galaxy-dist. I've set the tool-data-path in universe.ini to this new location. So, the indexes used by bowtie for example are retrieve without problem. But no build genome are available when we upload dataset or whit the pencil interface. Is there anoter file to configure the path of tool-data ? Thanks. Julie

2 1

Bug with workflow
by julie dubois 08 Jul '14

08 Jul '14

Hi all, I've a bug with the use of workflow. I've created my own workflow and since the latest update the workflow can be launched correctly but not completely!!! The first steps works with outputs on history, a job runs in job_working_directory for each of these steps. But for my final step : no job begin in job_working_directory so no data in history because the jobs don't exist. In my workflow the outputs are selected to be not hidden and the final step is connected with other steps. Any other one have this problem ? Thanks. Julie

4 5

removing wrapper version info from tools?
by Nikhil Joshi 08 Jul '14

08 Jul '14

Hi all, So I am trying to remove the version info (at the top of a tool page) entirely for all the tools. As I understand, those versions are the versions of the wrappers and not the tools themselves. Although I could change that, I would rather just not have the versions on the tool pages at all. We currently show all the versions of our tools on our landing page. Is there any way to remove the version part of the tool title entirely? I.e., if it originally says "Map with BWA for Illumina (version 1.0.0)", I just want it to say "Map with BWA for Illumina". - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

2 1