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tmp directory not cleaned up?
by Ryan Golhar 02 Jun '11

02 Jun '11

I just noticed a lot of files in my galaxy tmp directory. Since this isn't a system tmp directory, the system cron scripts don't clean it up. Is there a galaxy cron script that can be used to clean up this directory? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Further Progress
by ichorny＠illumina.com 02 Jun '11

02 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 02 Jun '11

02 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 02 Jun '11

02 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 02 Jun '11

02 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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MUMmer and TopHit filter
by Bossers, Alex 01 Jun '11

01 Jun '11

Our first tools arrived at the toolshed; The MUMmer genome comparison suite and a TopHit filter. Enjoy and we appreciate any feedback for improvement: http://community.g2.bx.psu.edu/tool/browse_tools?operation=tools_by_categor… Alex

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stdout and stderr while using pbs
by shashi shekhar 01 Jun '11

01 Jun '11

Hi All, if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem. can i check the standard error before displaying anything on browser. Reagrds shashi shekhar

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Accessing Data Library Template fields in tools?
by Duddy, John 01 Jun '11

01 Jun '11

I have my data in a data library and have a form template defined so I can enter the sample information. So, I import a data file into a history and want to run a tool on it. Can I pass the values of those form templates to my tool? Sort of line ${input.form_field_id} ? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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