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Galaxy Tool Creation Help
by James Boocock 12 Jul '12

12 Jul '12

Hi All, Just a quick question regarding galaxy tool creation. In the <command> tags Is it possible to get a datasets history number for the history the user initiated the job from? Seems unlikely, the reason I ask is that I have a tool that creates and output file for every input file and the program can take multiple inputs. It would be useful to be able to label the outputs related to the history number so the user could easily identify which output is for which file. Using the multiple output guide something like. primary_${id}_${history dataset number}_visible_txt Cheers James.

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Re: [galaxy-dev] Galaxy tool creation help
by James Boocock 12 Jul '12

12 Jul '12

Hi Guys Regarding my earlier question about history names. I found my answer on the wiki. ${input1.name} was what I was looking for. Cheers James.

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Tophat and bowtie jobs failed!
by A Ghanbarian 12 Jul '12

12 Jul '12

Hi, I have submitted tophat to run on two datasets yesterday morning. The jobs waited in the queue whole yesterday and the statues now show the output files being deleted. Not knowing the architecture that these services are running on, we also tried to submit couple of alignments for smaller datasets which both had the same faith. Now thinking there might be something wrong on the server. My user name is "Avazeh" and tophat jobs are still visible in the history, 52-55 and 60-63. Thanks for all the help, Avazeh

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Job doesn't runnig
by Amandin Talbot 12 Jul '12

12 Jul '12

Dear Galaxy Dev Team- I try to run a job with Tophat for Illumina (version 1.5.0) but in my history job always stay at "Job is waiting to run". I use the following parameters : RNA-Seq FASTQ file: FASTQ Groomer on upload dataset Reference Genome : build-in index : Chicken (Gallus gallus): galGal3 Full Mate-paired : Single-end TopHat settings : Defaults How should i do to make this job running ? Thanks in advance. ________________________ Amandin Talbot

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Tool migration errors
by Anthonius deBoer 11 Jul '12

11 Jul '12

I'm getting this error when I try to run the tool migration: sh ./scripts/migrate_tools/0003_tools.sh install_dependencies No handlers could be found for logger "docutils" Repositories will be installed into configured tool_path location ../shed_tools Adding new row (or updating an existing row) for repository 'freebayes' in the tool_shed_repository table. Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/migrate/common.py", line 150, in __init__ install_dependencies=install_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py", line 37, in __init__ self.install_repository( repository_elem, install_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py", line 258, in install_repository install_dependencies=install_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py", line 174, in handle_repository_contents tool_dependencies=tool_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/util/shed_util.py", line 1231, in handle_tool_dependencies tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/tool_dependencies/install_util.py", line 52, in install_package install_dir = get_tool_dependency_install_dir( app, tool_shed_repository, package_name, package_version ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/tool_dependencies/install_util.py", line 42, in get_tool_dependency_install_dir repository.installed_changeset_revision ) ) File "/home/tdeboer/code/galaxy_env/lib/python2.6/posixpath.py", line 67, in join elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' Any ideas? Thanks Thon

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Where are the datatype associations stored?
by Anthonius deBoer 11 Jul '12

11 Jul '12

Hi, I had some more bad luck trying to install the GMAP stuff from the TOOLSHEd but revision 10 is broken since it does not allow you to select a section and just stores the programs in the main tree... But when I tried to remove the tool I got the following error for every run, since the sniffers where still looking for a module called GMAP... Which table should I nuke to get rid of this association? Where are the datatype associations stored? There does not seem to be an XML file for this, so I hope i can just remove some lines from the postgres database table but there are no obvious table names I can find... WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap Thanks

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javascript
by Cathy Riemer 11 Jul '12

11 Jul '12

Hi all, I just now tried visiting Galaxy main with my browser's javascript turned off. Formerly the left Tools panel would appear with all of the sections expanded, however now it is empty except for "Workflows". Also, some of the top menu bar items work without scripting, but others (including Help and User) do not. Ideally Galaxy would be usable without scripting, but if that is not feasible then I suggest checking whether javascript is available (as many other sites do) and displaying a prominent explanatory message if it is not. This would be much more helpful than an inexplicably near-empty tool panel and broken menus. In case it is relevant, I'm running Firefox 3.6.23 with the NoScript extension (2.4.7), on CentOS Linux with kernel 2.6.18-238.12.1.el5. Thanks, -Cathy

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is there a way too automatically select references based on the genome of the dataset?
by Langhorst, Brad 11 Jul '12

11 Jul '12

I would like the reference list to be automatically selected based on the dbkey of the selected input... I think I've seen this, but I can'f seem to find an example. Anybody know? Should be some easy jquery i guess. Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

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Output file permissions different pbs:/// VS local:/// job runners
by Rob Syme 11 Jul '12

11 Jul '12

Hi all. When I run the FastQC tool using the default local job runner, it produces a folder of files with permission 664: <snip> -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 error.png -rw-rw-r-- 1 galaxy galaxy 7.5K Jul 5 17:29 fastqc_data.txt <snip> When I switch to using the(local) pbs queue, it produces a folder with permissions 600: <snip> -rw------- 1 galaxy galaxy 15K Jul 6 09:10 duplication_levels.png -rw------- 1 galaxy galaxy 1.6K Jul 6 09:10 error.png -rw------- 1 galaxy galaxy 8.8K Jul 6 09:10 fastqc_data.txt <snip> The final dat file (in database/files/000/dataset_xx.dat) is fine, it's just the files in the corresponding folder (database/files/000/dataset_xx_files/*) that have the incorrect permissions. These more restrictive permissions mean that the files cannot be read by apache, resulting a bunch of broken links when viewing the tool's output. Does anybody know why this might be happening or how to resolve it? Many thanks. -r

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Galaxy cleaning up after it self after jobs fail
by Anthonius deBoer 11 Jul '12

11 Jul '12

I am running galaxy on a system that normally runs all jobs on the cluster, but some jobs need to be run locally... But when I restart galaxy when these jobs are running, those jobs fail (and I am fine with that)... But then when I check the logs, I see a lot of this kind of errors and the word CRITICAL scares me a little... It complains about certain directories not being empty (although they look empty to me when I look at them).... But if it needs to clean up should it not expect stuff to be in those working directories? And why is this a critical error and why don't those directories get removed anyway...It clutters my database and I fear this was the reason for weird behaviour I saw earlier, since it may re-use some of these directories after a while ? galaxy.objectstore CRITICAL 2012-07-05 16:57:24,964 /mnt/ngs/analysis/tdeboer/galaxy-data/database2/job_working_directory/003/3350 delete error [Errno 39] Directory not empty: '/mnt/ngs/analysis/tdeboer/galaxy-data/database2/job_working_directory/003/3350' Thanks Thon

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