June 2011 - galaxy-dev - lists.galaxyproject.org

Further Progress
by ichorny＠illumina.com 01 Jun '11

01 Jun '11

Have you made any additional progress on implimenting "running DRMAA(sge) jobs as different user" (i.e. selecting which user)? Also, have you found a way to integrate Linux usernames with Galaxy user names? Thanks, Ilya

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Error getting to http://galaxy/user/create on local instance
by Dave Walton 01 Jun '11

01 Jun '11

We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave

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Re: [galaxy-dev] Script which creates users
by Chorny, Ilya 01 Jun '11

01 Jun '11

Can someone point me to the script that adds users to the user database? I want to check to see if a linux user name exists and add create that account if it doesn't. BTW, has anyone else implemented this? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Out of Memory Error (Galaxy Local Instance) - File Download
by John David Osborne 01 Jun '11

01 Jun '11

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Dynamic default values
by Peter Cock 01 Jun '11

01 Jun '11

Dear all, I was thinking about how to improve some of my tools and wondered if there is any way to have dynamic default values for parameters (depending on other parameters). Obviously this won't make sense in all cases, but as a specific example, consider my Venn Diagram tool: https://bitbucket.org/peterjc/galaxy-central/src/9f66c5d1fca8/tools/plottin… I have separate parameters for each dataset (file input) and its caption (text input). Like so: <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/> <param name="lab" size="30" type="text" value="Group" label="Caption for set"/> Is something like this possible (or generally useful?) <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/> <param name="lab" size="30" type="text" value="$set.name" label="Caption for set"/> i.e. The default value of the label text parameter "lab" would be the human friendly name of the associated data file parameter "set". I'd expect changing the file to also change the text box. I have thought of a workaround, but not yet tried it: Use the empty string as the default, and use an if statement in the Cheetah template for constructing the command line string. Thanks, Peter

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Meaning of ${on_string} in tool XML files
by Peter Cock 01 Jun '11

01 Jun '11

Hi all, What is the official mean/use of ${on_string} in Galaxy tool XML files? This variable name appears in lots of tools, but does not seem to be documented here: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Are there any related variables which also need documenting? I've checked the mailing list (at least, for as long as I've been subscribed), and done a quick search with Google, but found nothing informative. Thanks, Peter

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