galaxy-dev April 2013

galaxy-dev@lists.galaxyproject.org

87 participants
164 discussions

REST API
by Marc Logghe 02 Apr '13

02 Apr '13

Hi, I was trying to run workflows from the command line using workflow_execute.py in /scripts/api. According to the documentation, the commandline should look like: python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f I understand that 'hda' refers to the src of the input data, in this case being the history. However, it is not clear to me what 38 is actually referring to. Is it the step number ? Is it the id shown in the JSON response code of <galaxy_url/api/workflows/<workflow id> ? E.g "535" in: {"url": "/galaxy/api/workflows/f7bb1edd6b95db62", "inputs": {}, "steps": {"535": {"tool_id": "iep", "input_steps": {}, "type": "tool", "id": 535}}, "id": "f7bb1edd6b95db62", "name": "test_workflow"} What is "inputs" and why is its value empty {} ? If a tool step has multiple input parameters, how can you refer to the correct parameter using the 'step=src=id' syntax ? Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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April 2013 Galaxy Update
by Dave Clements 01 Apr '13

01 Apr '13

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Galaxy April 1, 2013 Distribution
by Jennifer Jackson 01 Apr '13

01 Apr '13

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GCC2013 Oral Presentation Abstract Submission Closes 12 April
by Dave Clements 01 Apr '13

01 Apr '13

Hello all, This is just a reminder that the *deadline for submitting an oral presentation abstract is 12 April, which is less than two weeks away*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. Thanks, Dave C On Sun, Feb 24, 2013 at 7:40 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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galaxy-dev April 2013