October 2013 - galaxy-dev - lists.galaxyproject.org

Download URL not accepted in tool_dependencies.xml
by Joachim Jacob | VIB | 01 Oct '13

01 Oct '13

Hi all, The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package. The error upon uploading the tool to my toolshed: ************** Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149 ************** The tool_dependencies.xml file: ************** 1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/…</action> 7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file"> <source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> ************** Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Dynamic_options + DataToolParameter + refresh_on_change_values + multiple="true"
by Y. Hoogstrate 01 Oct '13

01 Oct '13

Dear Galaxy user, I'm working on a interface where the user can choose multiple data files using <param name="data_selection" type="data" multiple="true" />. Although I didn't find details about this in the manual, it does work. The next step in the interface are two select boxes (<param type="select" samples" multiple="true" dynamic_options="copy_selected_data_names(data_selection)" />) which allow further selection on the data chosen in "data_selection". I created a small python script that copies the entries selected in "data_selection" as follows: def copy_selected_data_names(DataToolParameter_multiple_object): items = [] if(DataToolParameter_multiple_object != NULL): if(type(DataToolParameter_multiple_object) == type([])): ## If it is a list for g in DataToolParameter_multiple_object: items.append([g.name,g.file_name,False]) else: ## If it isn't a list items.append([DataToolParameter_multiple_object.name,DataToolParameter_multiple_object.file_name,False]) return items I noticed that once only one single object is selected, the DataToolParameter returns directly one HistoryDatasetAssociation object. Once several are selected, it returns a list with HistoryDatasetAssociation objects. I think this is not correct; the DataToolParameter is a object where multple is set to "true" so it should always return a list even if none or 1 object is selected. Nevertheless, this part of the code works. However, the update of the dynamic_options="copy_selected_data_names(data_selection)" only takes place whenever new objects (in repeat blocks) are added or removed elsewhere in the interface. Thus, the copying of the content doesn't take place when the selection has changed. My question is: is there a way to make dynamic_options="" update whenever the selection in "data_selection" has changed? I checked the code and I found some variables in the DataToolParameter class that may have something to do with it: self.refresh_on_change = False self.refresh_on_change_values = [] But I'm not able to solve the puzzle on my own. Is there anyone who can help in this direction? Thanks in advance!

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Dynamic data library
by Cole, Nathan (NIH/NCI) [C] 01 Oct '13

01 Oct '13

Hello, we've set up a local Galaxy instance in our genotyping and next-gen sequencing lab with local Apache LDAP (AD) integration, NFS mounts to a large NAS, and cluster integration coming. Do to the high volume of samples and staff that will be using the system, I want to set up data libraries (without copying to Galaxy). This is obviously no problem the first time, however I was wondering if there was a way to make a library, added from a system path, be dynamic so that it would stay synchronized with the underlying file structure? If a try dynamic library is not possible, is there a method for adding files to an existing library via that same system path that would not duplicate all of the original files in the data library? I did some scouring of the list and found some old unanswered questions and some things tangentially related topics, but I was unable to find a true answer or solution to my problem. Any information on how to do the tasks above or other solutions to provide the same functionality would be greatly appreciated. Thanks, Nathan

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Problem with get data/uploading file.
by Luobin Yang 01 Oct '13

01 Oct '13

Hi, guys, Recently I found the Upload File tool under the Get Data category runs forever on my locally installed Galaxy system. It worked fine for a long time, but now it's not working anymore. Have you guys experienced similar things? Thanks, Luobin

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RNAseq Map with Top Hat job in queue 4 days, 'waiting to run"
by Theresa Stueve 30 Sep '13

30 Sep '13

Greetings, I would like to map some RNAseq data in Top hat in Galaxy Main- I only have 2 files but both have have been in queue 'waiting to run' since last Thursday (9/26)? I have a data meeting this Thursday and am gonna get trounced can you advise? history is below is there another galaxy I can try perhaps? I do appreciate that you all are expanding the universe -- Theresa Ryan Stueve 510-225-8894 (text better than voicemail for quick response)

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bwa indexing not automatic?
by Jennifer Jackson 30 Sep '13

30 Sep '13

Hi Joshua, Just to double check, you are running the latest stable distribution? There are a few different BWA wrappers in the tool shed, maybe you are using a different one than previously? Using a custom reference genome from the history with bwa is possible with the wrapper with the owner "devteam" (assuming Galaxy is installed where there are suitable resources - same as command line bwa). If you want to try again and report back any ongoing issues, please use the galaxy-dev(a)bx.psu.edu mailing list to reach the development community (drop galaxy-user(a)bx.psu.edu from the to or cc). Thanks, Jen Galaxy team On 9/27/13 7:37 PM, Joshua Orvis wrote: > I installed a new copy of galaxy today and then added the bwa_wrappers > tool. After I upload my reference genome and left/right reads I get > output like this each time I try to run bwa for illumina: > > The alignment failed. > Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 > [bwa_aln] 38bp reads: max_diff = 3 > [bwa_aln] 64bp reads: max_diff = 4 > [bwa_aln] 93bp reads: max_diff = 5 > [bwa_aln] 124bp reads: max_diff = 6 > [bwa_aln] 157bp reads: max_diff = 7 > [bwa_aln] 190bp reads: max_diff = 8 > [bwa_aln] 225bp reads: max_diff = 9 > [bwt_restore_bwt] fail to open file '/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'. Abort! > /bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat > /tmp/tmpMuj4l2/tmpUIdxXT > If I manually do the 'bwa index' command on dataset_4.dat it works but in the past this seemed to happen automatically. Any clue what's going on here? > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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