April 2012 - galaxy-dev - lists.galaxyproject.org

<repeat> tag
by Unknown 06 Apr '12

06 Apr '12

Hi all, This is a question about <repeat> tag. How can we pass the repeat tag parameters nested within another repeat tag to command tag? For example,I have a front end like the following <conditional name="cond1"> <when value="something"> <repeat name="rpt1".........> <param1........> <repeat name="rpt2"...........> <param2............> </repeat> </repeat> </when> </conditional> How can I access the param2?

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<repeat> tag
by Unknown 06 Apr '12

06 Apr '12

Hi all, This is a question about <repeat> tag. How can we pass the repeat tag parameters nested within another repeat tag to command tag? For example,I have a front end like the following <conditional name="cond1"> <when value="something"> <repeat name="rpt1".........> <param1........> <repeat name="rpt2"...........> <param2............> </repeat> </repeat> </when> </conditional> How can I access the param2?

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Output files from Galaxy
by Xu, Jianpeng 05 Apr '12

05 Apr '12

Hi, I have installed the local galaxy. I am trying to run some programs. I have a question now: If I run a program and the output file will be in the history. If I want to do something with the output file, it looks like I have to download it at first. Is there a way to do something with the output file without downloading it ? Where does the output file store ? Is there a way to configure to put the output file under a specific directory ? Thanks a lot. Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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directories as inputs/dataset file extensions
by Aaron Gallagher 05 Apr '12

05 Apr '12

Hi, I've been working off of a local instance of Galaxy (6799:40f1816d6857) to develop tools and I'm running into some issues which I'm not sure how to resolve idiomatically. First, some of the tools I'm trying to write Galaxy wrappers for take a directory as input. The directory contains some metadata and some related files (a FASTA alignment; a Newick tree; etc.). Originally I tried making a data type that was a .tar.gz'd directory and a converter that would untar it to a directory by doing approximately `rm $output; mkdir $output; tar xf $input -C $output`. This was causing errors in Galaxy; I can get these if it would be useful, but I figured that this is probably an unsupported thing anyway. The way that I'm handling it now is to untar the archive every time that the tool is run, but it seems like there's probably a better way of setting this up. Second, these tools also expect their inputs to have a meaningful file extension, but it seems like the filenames that Galaxy gives to the tool all just have ".dat" as the extension. I was getting around this by doing `ln -s $input input.ext`, but again, this seems suboptimal. It's also complicated by that some of these programs can take a FASTA or Stockholm alignment, but decide which parser to use by the extension. I'd like to be able to support both, but it seems like that would require somehow getting the file type out of the metadata and doing some sort of check against that. I've seen some mailing list posts that talk about doing the same symlink trick, but I'm kind of hoping that there's some better method available now. Thanks for any insight into writing idiomatic Galaxy tools, ~Aaron

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Data library
by Xu, Jianpeng 05 Apr '12

05 Apr '12

Hi, I have installed the local galaxy. And I have tried to use the data library to upload some CEL datasets. However, it occurred an error when I use data library to add datasets. It showed: Miscellaneous information: The uploaded binary file contains inappropriate content error Do you know how to fix it ? Best, ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Bus error
by Johannes Eichner 05 Apr '12

05 Apr '12

Dear Galaxy Dev-Team, I set up a local Galaxy instance at the University of Tuebingen, Germany. It runs on a virtual machine, which submits jobs to a small cluster consisting of three nodes running Ubuntu 10.04 (64bit). Occasionally, when I submit a job via Galaxy, the respective history item stays grey and the job is not passed to the cluster. When this happens, Galaxy crashes with the error message "Bus error": galaxy.jobs INFO 2012-04-05 14:29:16,779 job 1132 dispatched 134.2.172.47 - - [05/Apr/2012:14:29:16 +0200] "GET /history HTTP/1.1" 200 - "http://ratest4:8080/tool_runner/index" "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:11.0) Gecko/20100101 Firefox/11.0" Bus error Today, I updated our Galaxy instance to the latest version from the "galaxy-dist" repository, but the problem is still present. I would very much appreciate your help on this issue. Kind regards, Johannes -- Dipl.-Inf. (Bioinf.) Johannes Eichner Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 / 29 78970 Fax: (+49/0) 7071 / 29 5091

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problem with data libraries
by Andreas Kuntzagk 05 Apr '12

05 Apr '12

Hi, I created a data libraries and imported files into it (from local path with symlinks) There are 1500 files in that directory. Now when I attempt to view the library I get this error: Error attempting to display contents of library (test lib): 'NoneType' object has no attribute 'dataset'. What is the problem here? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Can anyone give an example of how to setup the apache2 to handle external user authentication(against postgresql db)?
by JIE CHEN 05 Apr '12

05 Apr '12

Dear all, I followed the instructions under the link http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy to set up a Apache proxy to Galaxy. I have done with the section of basic configuration and it works very well. However when I move to the next section: external user authentication, I found out that the sample given on that page is only suitable for the case when using file-based(htpasswd) authentication. My Galaxy instance is connected to a postgresql database and store all its user information there. Can anyone give some instructions how to configure apache to authenticate users againest postgresql db? (I did do some searchings and found out that it seems we have to enable mod_authn_dbd. I enabled it already, but after that i don't know how to add/edit the directives to make it work properly) Thanks in advance. Cheers, Tyler

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Re: [galaxy-dev] directories as inputs/dataset file extensions
by Aaron Gallagher 05 Apr '12

05 Apr '12

On Apr 4, 2012, at 11:35 AM, Langhorst, Brad wrote: > Given that it describes where the rest of the files are, maybe it would work to pass only the CONTENTS.json file. > Then you can just build your references in a directory structure on a shared file system and keep absolute paths in the CONTENTS.json file. > > If you don't want to modify the tool to accept only the json file, you could write a simple wrapper to read the json and symlink everything into place before calling your tool. I think this is the simplest solution for now. > This is somewhat akin to the reference area galaxy uses to store reference sequences (and their various indices, formats, annotations etc). > It might be possible to modify galaxy's reference infrastructure to present these pre-built reference packages in the same way a user chooses hg19, or E. coli K12. The parse JSON option looks easier to me This seems like something I should look into, at least. These don't come with Galaxy, do they? > I'm not aware of other galaxy tools that pass "directories" in this way, but they may exist. I haven't found anyone who seems to be doing the same thing, at least. > I don't know if you intended to go off-list, feel free to go back on if you want to. My mistake; I resent my e-mail back on the list as well, but it's pending moderation at the moment. ~Aaron

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Best practice about including java.jar in toolshed tool
by Joachim Jacob 04 Apr '12

04 Apr '12

Hello, I am looking for the way to go to include JAVA jar or classes into a Toolshed tool. I noticed that JARs are gathered in galaxy-dist/tool-data/shared/jars. e.g. below: java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" What I did, I placed the java class next to the tool xml file, and called in the xml file the java class, using a static path (see below). e.g. <command> java -cp *~/galaxy-dist/tools/joatools* BaseCalls3 -l `head -2 $input | tail -1 | wc -c` -o $output_basecalls -q $output_qualities $input </command> Can I use a GALAXY environment variable to refer to the directory of the tool? If so, then I can share with Toolshed my tool xml and java class file. Or is there another method I should follow? Kind regards, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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