galaxy-dev August 2013

galaxy-dev@lists.galaxyproject.org

116 participants
210 discussions

Velvet optimizer: Running two long paired files.
by Perez, Ricardo 02 Aug '13

02 Aug '13

Dear all, Today when running velvet oprimizer vlsci, we encountered that if you use two long files as input then the output is a file that its description is "no peek". However when I run the files seperately the velvet optimizer seems to work fine. I am not sure if this is a bug or not. Thank you for your time, --Ricardo Perez

2 1

Error message
by Mark Edward Fabreag 01 Aug '13

01 Aug '13

Good day! While I was uploading the file (through FileZilla), I encountered this message box: [image: Inline image 1] Will this affect uploading process? Thank you.

2 1

extract metadata
by Christian Dreischer 01 Aug '13

01 Aug '13

Hi there, I'm looking for an elegant way to extract the metadata for a Galaxy history item from a PostgreSQL database. My special interest lies in the path to the output file and the input parameters. Has by any chance anybody already done this and a ready to use python script at hand? ;) Thanks, Chris

1 0

enable to edit pages
by Philipe Moncuquet 01 Aug '13

01 Aug '13

Hi guys, Since the last update of Galaxy. We are enable to edit pages on our local instance. Pages can be viewed without problems but not editing. The server error we get is as foolow, any advice would be greatly appreciated. URL: http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33… Module galaxy.web.framework.middleware.error:*149* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.recursive:*84* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*98* in decorator >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.page:*446* in edit_content >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* trans*.*fill_template*(* "page/editor.mako"*,* page*=*page *)* Module galaxy.web.framework:*957* in fill_template >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*fill_template_mako*(* filename*,* ****kwargs *)* Module galaxy.web.framework:*969* in fill_template_mako >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* template*.*render*(* ****data *)* Module mako.template:*296* in render >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> ****_kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> callable_*(*context*,* ***args*,* ****kwargs*)* Module _base_base_panels_mako:*125* in render_body >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> __M_writer*(*unicode*(*self*.*center_panel*(**)**)**)* Module page_editor_mako:*196* in render_center_panel >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> __M_writer*(*unicode*(*page*.*latest_revision*.*content*.*decode*(*'utf-8'*) **)**)* Module encodings.utf_8:*16* in decode >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* codecs*.*utf_8_decode*(*input*,* errors*,* True*)* *UnicodeEncodeError: 'ascii' codec can't encode character u'\u2019' in position 1709: ordinal not in range(128)* * * Regards, Philippe

2 1

Next Galaxy Release date (and Tool Shed update)?
by Peter Cock 01 Aug '13

01 Aug '13

Hi all, Is there a target date for the next Galaxy release, or should that differ, the next update to the main Tool Shed? I'd like to start using reStructuredText README.rst files in my tools which render much more nicely on the Test Tool Shed, but are currently ignored on the Main Tool Shed (since it doesn't yet have the updates to look for and display *.rst files). Thanks, Peter

3 4

What are these called and where can I learn about them...
by Gordon Botha 01 Aug '13

01 Aug '13

Hi all Apologies if I am in the wrong channel to post this. I have been using Galaxy for a couple of months now and I'm still finding my way around the mass of info Some of the XML config file tags have a string interpolation type of variable such as ${tool.name} in: label="${tool.name} on ${on_string}: insertions" Where can I read up more on these and learn what others exist? I tried http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax and found a titbit at the end of the page but nothing more. Thanx gordon

1 0

fail to run gatk
by Karen Chait 01 Aug '13

01 Aug '13

Hello, I am trying to run GATK on a local galaxy installation. I get the following error: ##### ERROR ---------------------------------------------------------------------------- -------------- ##### ERROR A USER ERROR has occurred (version 1.5-21-g979a84a): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Walker requires a reference but none was provided. ##### ERROR ---------------------------------------------------------------------------- -------------- I choose a fasta file from the history. When I try to run it directly from the server it works fine but not through the galaxy interface. I guess something is incorrect in the wrapper. Any advice? Thanks, Karen

1 0

Downsampling of SAM/BAM files
by Alexander Kurze 01 Aug '13

01 Aug '13

Hello, I am running a local galaxy server and tried to add the downsampling script for SAM/BAM files from Brad Longhorst which I found on Github. It uses a modified picard_wrapper.py. I get everything running except that the end file shows up empty. I realised when looking at the log file that the Input directory differs from the output directory also instead of adding a .data file it produces a .metrics.txt file. Does anyone know how to fix this, or does anyone have another script which can be used on Galaxy for downsampling SAM/BAM files? Thanks a lot, Alex

1 0

job_conf.xml questions
by Ido Tamir 01 Aug '13

01 Aug '13

Hi, I work myself through the job_conf.xml and have a question: a) In your advanced example you have: <destination id="remote_cluster" runner="drmaa" tags="longjobs"/> <destination id="real_user_cluster" runner="drmaa">  <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> Does this mean that remote_cluster jobs can not be killed unless I add the 3 scripts to this destination? Or does this have to do with the "run jobs as real user" that I don't need currently. I am using the galaxy user for all jobs for the moment? To phrase this differently: Do I need these three scripts? b) Can I set a wall time limit for only for my local runners? like: <destination id="local" runner="local"/> <param id="Resource_List">walltime=72:00:00</param> </destination> When I set it in limits, will it work for local runners and then I have to override it in every destination? thank you very much, ido

2 1

importing data from other public websites into galaxy
by Prasun Dutta 01 Aug '13

01 Aug '13

Hi, I wish to import data into my local instance of galaxy from another website. Kindly let me know how to achieve that and what all is required. I want to import data from a chemoinformatic database (mainly compound structures) into galaxy and run my own analysis tools on them. Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

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galaxy-dev August 2013