Re: [galaxy-dev] Possible to re-use toolconfig xml files outside Galaxy?
Hi Alex, Much thanks for your input. On 07/13/2011 02:31 PM, Bossers, Alex wrote: as far as the xml goes. Yes it usually is accompanied by a py perl or bash script. However you could extract at least the user configurable options to gather input/output and setting parameters from the definition in the xml. Well, I'm just afraid that in too many occations, the input param flags and order for the accompanying (py/sh/perl) script might not be identical to the command line tool itself (or do the toolconfig generally avoid changing the flags and their order?). Best // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -- E-mail: samuel.la...@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se ___ 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/
Re: [galaxy-dev] Installing tools with dependencies using mi-deployment scripts
Hi Mattias,
PyCogent is not currently being installed as part of mi-deployment, so the
method for installing it should be added (if you do so, please consider
issuing a pull request on bitbucket so it can be added to the project).
When it comes to composing $PYTHONPATH to include the reference to PyCogent
via Qiime's env.sh - this should be done as part of the Qiime installation
method in mi-deployment (something like export PYHTONPATH=path where
PyCogent was installed; export PATH=...).
Sourcing of the tool's env.sh script is prepended to the execution command
when running the tool so the appropriate environment settings will be loaded
before the tool is run.
Enis
On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander
m.dehollan...@nioo.knaw.nl wrote:
Hello,
I am trying to add tools (PyCogent, Qiime) to a Cloudman image using the
mi-deployment scripts. Qiime depends on PyCogent and it needs to be
accessible on the python path, otherwise I get an error:
PyCogent not installed but required. (Is it installed? Is it in the
current user's $PYTHONPATH or site-packages?)
Is there a way to add the paths in env.sh to the sys.path during
installation using tools_fabfile.py?
All the tools are in /mnt/galaxyTools/tools.
I tried the DependencyManager from galaxy but then I only receive the
path to the env.sh file:
In [43]: dependency_manager.find_dep('blast')
Out[43]:
('/mnt/galaxyTools/tools/blast/2.2.25/env.sh',
'/mnt/galaxyTools/tools/blast/2.2.25',
'2.2.25')
Is there a smarter way to add files to the PYTHONPATH during the
execution of tools_fabfile.py?
Thanks,
Mattias
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
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Re: [galaxy-dev] toolExample.pl script bug report
Casey: This 'elegant' script has been fixed. Thank for poiting this out! a. Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Jul 12, 2011, at 11:51 AM, Casey Bergman wrote: Dear Galaxy Team - We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial In our hands, this script only works on fasta files that contain 1 sequence, and reports gc content only for the first n-1 sequences. If you could confirm this and modify if possible, this might help other users. All the best, Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman Email: casey.berg...@manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/ ___ 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/ ___ 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/
[galaxy-dev] Sending Data to Galaxy
Hey Galaxy developers! I was wondering if anyone knows how to send data to a local galaxy instance from another server (I'm interested in sending a BAM file to Galaxy). I see that UCSC and others have done it but couldn't find anything about the API doc they are using... Looking at the request headers from UCSC, I see that this request: tool_id:bx_browser URL:http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables hguid:883956 db:hg18 org:Human hgta_table:seq hgta_track:gold hgta_regionType:genome hgta_outputType:primaryTable position:chr10:90997300-90997350 hgta_doTopSubmit:get output hgsid:62857 hgta_doGalaxyQuery:Send query to Galaxy has been sent to: http://main.g2.bx.psu.edu/tool_runner Is this all needed? If so how is the URL to the data file passed to Galaxy? Many thanks! Amir___ 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/
Re: [galaxy-dev] more cleanup scripts messages
Hello Assaf, Thanks for this patch as well. I've added it in change set 5792:a3fc507f2b42. Greg Von Kuster On Jul 13, 2011, at 1:53 PM, Assaf Gordon wrote: Hi Greg (again), This patch adds messages for the purge histories step: 1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong). 2. in info_only mode, a message is printed about each deleted history 3. in info_only mode, a message is printed for each HDA that is checked 4. The message for HDA is changed to include the associated dataset id. Comments are welcomed, -gordon galaxy_cleanup_purge_histories.patch___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Sending Data to Galaxy
Hi Amir, If you are interested in adding a new datasource, take a look at: http://database.oxfordjournals.org/content/2011/bar011.full http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources If you just want to add a file from an http/ftp location, take a look at the Upload tool, under the Get Data tool menu. Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Jul 14, 2011, at 1:54 PM, Amirhossein Kiani wrote: Hey Galaxy developers! I was wondering if anyone knows how to send data to a local galaxy instance from another server (I'm interested in sending a BAM file to Galaxy). I see that UCSC and others have done it but couldn't find anything about the API doc they are using... Looking at the request headers from UCSC, I see that this request: tool_id:bx_browser URL:http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables hguid:883956 db:hg18 org:Human hgta_table:seq hgta_track:gold hgta_regionType:genome hgta_outputType:primaryTable position:chr10:90997300-90997350 hgta_doTopSubmit:get output hgsid:62857 hgta_doGalaxyQuery:Send query to Galaxy has been sent to: http://main.g2.bx.psu.edu/tool_runner Is this all needed? If so how is the URL to the data file passed to Galaxy? Many thanks! Amir ___ 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/ ___ 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/
[galaxy-dev] fyi: can't upload to toolshed
Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here) ___ 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/
