June 2010 - galaxy-dev - lists.galaxyproject.org

get job update_time & update_time-create_time as label in history
by Michael Pheasant 26 Jun '10

26 Jun '10

Hi How can i get the job total run time (update_time - create_time) into the label in the history? Something like: <data format="..." label="${tool.name} on ${on_string} ${update_time-create_time}"/> But this gives me the error: NotFound: cannot find 'update_time' I'm not sure what the fully qualified name of update_time would be. I think its in the job table. Cheers M -- Dr Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 6, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org

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Re: [galaxy-dev] Developing Tools With Java
by Jesse Erdmann 25 Jun '10

25 Jun '10

Hi, In the past, I've done something like this: <command> #set $jar_dir = "/mydir/jars/" java -cp $jar_dir/my_jar.jar:$jar_dir/my_second_jar.jar MyClass $input </command> However, it looks like you can set a jar directory. Here's the relevant bit from a recent update: 4) Add a jar directory / bin which is accessible to tool configurations by specifying e.g. '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired jar which has been placed in / linked to 'GALAXY_ROOT/tool-data/shared/jars' (by default; $GALAXY_DATA_INDEX_DIR can be configured to point elsewhere [value of 'tool_data_path' configuration variable in universe_wsgi.ini]). The setup.sh script has been modified to create this directory when not present. I haven't tried using this, so I'm not entirely sure how a tool would use a jar in the shared directory. On Fri, Jun 18, 2010 at 7:40 AM, Elie Freilich <Elie.Freilich(a)gmail.com> wrote: > Hello, > > I just started working with developing a tool for Galaxy; I have been > programming it in Java. However, when it came time to implement my > tool into Galaxy, I was unable. When I try to run it normally, it > works. However, in Galaxy, when I try to use the JAR file, it produces > a java.lang.NoClassDefFoundError and a > java.lang.ClassNotFoundException. > > As it seems rather meaningless to be setting a classpath in an > abstract framework like Galaxy, is there a simple way to run Java JAR > files? I tried a "-jar" argument, but I can't put in an argument > before the filename. Should I be using the ".class" files instead of > the JAR files? Should the format in the XML file be <command > interpreter="java"></command>? > > Thanks so much, > Elie > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev > -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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Workflow Post Job Actions and Cleanup scripts
by Dennis Gascoigne 25 Jun '10

25 Jun '10

The post-job actions feature is great. Just a question though, do hidden jobs get deleted using the cleanup scripts? If not - can we do that? If so, how? Cheers -- Dennis

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Re: [galaxy-dev] Error when dowloading large compressed data library
by Nate Coraor 24 Jun '10

24 Jun '10

padioleau wrote: > Hi Nate, > I'm working with a local version and we have tried with all the > compressed format. Can you ensure that: debug = False use_lint = False use_interactive = False use_profile = False is set in your universe_wsgi.ini file? > > Regards. > > Ismael > > > On Wed, 23 Jun 2010 14:52:00 -0400, Nate Coraor <nate(a)bx.psu.edu> wrote: >> padioleau wrote: >>> Dear Galaxy developers, >>> >>> When I try to download a large data library (from the Data Libraries > tab) >>> as any compressed file I encounter this error: >>> >>> ### >>> Proxy Error >>> The proxy server received an invalid response from an upstream server. >>> The proxy server could not handle the request POST /galaxy_dev/ >>> library_common/act_on_multiple_datasets. >>> >>> Reason: Error reading from remote server >>> ### >>> >>> If I download file per file (no compression) it's working. >> Hi Ismael, >> >> Is this on one of our public servers (Galaxy Main or Test)? If so, >> which download format option are you choosing? >> >> Thanks, >> --nate >> >>> Ismael >>> >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev >

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is it possible to upload files to different local directories based on the galaxy upload.py script?
by amenda lee 24 Jun '10

24 Jun '10

Hi; Is it poosible to upload files to the different local directories by Galaxy upload.py script? It seems to upload all files to the same directory based on the file path in universe_wsgi.ini file. if yes, what part of upload.py needs to be edited? also is it possible to keep name of uploaded file unchanged? Thanks in advance. Amenda Lee

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Cleaning Data Sets
by Chris Zaleski 24 Jun '10

24 Jun '10

Greetings, Could you please help me clarify the system of cleanup scripts? I've read the documentation on the wiki page regarding these scripts, but some of it is still unclear. My basic issue is - I've never had a single file deleted from disk. The docs state you should run the scripts in the following order (which is what I am doing): delete_userless_histories.sh purge_histories.sh purge_libraries.sh purge_folders.sh purge_datasets.sh Although there are indeed files which qualify for deletion, my 'purge_datasets.log' always shows "Purged 0 datasets". Files on disk never seem to be deleted. I thought perhaps the additional script "delete_datasets.sh"is necessary. However the docs state "If it is desired that datasets be removed before their outer container (history, library/library folder) has been deleted, the delete_datasets.sh script can be used before the purge_datasets.sh script". ...I don't want datasets to be removed before their outer container. I just want them to be removed when the container(s) *have* been deleted. I did try running "delete_datasets.sh" once. It's log showed a huge number of datasets being deleted. But the next day when "purge_datasets.sh" ran... still nothing was actually deleted. Perhaps I simply don't understand the process correctly. Could you please help? Thanks very much, Chris

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the display of bam files from galaxy behind apache is not working
by Terrence Barrette 24 Jun '10

24 Jun '10

Hi, I can't see the data at ucsc when I upload a bam file and try to display it. The track arrives at ucsc. I see GET /display_application/... and 200 and bytes in the httpd/access_log I see GET /display_application/... in the paster.log But I don't see the seq reads at the ucsc browser. Some background information: I am setting up our local galaxy server. The server is redhat 5. The IP is external and whether firewall is up or down is immaterial in the behavior. The galaxy install is running at localhost:8080. There is the default redhat apache running in front of galaxy with the rewrite rules enabled for static and all traffic to port 80. Apache security is not enabled (yet). The dedicated galaxy user and group is running galaxy. Thanks, Terry ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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June 21, 2010 Galaxy Development News Brief
by Greg Von Kuster 23 Jun '10

23 Jun '10

The latest news brief is available at the following link. You are strongly encouraged to upgrade to the revision detailed in this news brief as it contains important security fixes for data libraries. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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How do I contribute a bug-fix?
by Pablo Cingolani 23 Jun '10

23 Jun '10

Could someone please tell me (or point me to) the proper procedure to contribute a bug fix? Thank you :-) P.

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More flexible use of Sun Grid Engine by Galaxy
by Peter van Heusden 23 Jun '10

23 Jun '10

Hi there At the moment Galaxy's choice of Sun Grid Engine settings are done on a per-tool basis - that is, you can define different queues and projects on a per-tool basis. However, I've got two use cases that currently aren't supported. 1) Per-user settings. The SGEJobRunner potentially has access to user information (via the job.session_id), and while all jobs get run as user galaxy, per-user settings could be simulated by mapping Galaxy users to SGE projects. Then the SGE admin can do load-balancing, etc on a per-project basis. For a site with a relatively small and static set of users this could work. Alternately you need to map Galaxy users to SGE users - this is much trickier, requiring elevated privileges and thus probably a separate job runner daemon. 2) Queue selection. Again this could be done on a per-tool basis, but usage patterns don't always support that. So for example, our site has two queues - a long running one and a short running one. Certain resources are reserved for only the short running queue's usage. How to select a different queue for jobs raises a bit of a design problem for me - effectively you're telling Galaxy "I want to run this workflow, but with this extra parameter" - its almost like having a "meta parameter" since clearly you don't want to have queue selection as an input for any particular tool. So I'd be interested in the Galaxy team's input as to how best to address these two use cases. Thanks, Peter

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