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

Deleting tmp files
by Ciara Ledero 20 Apr '12

20 Apr '12

Hi all, I would just like to ask if the tmp files in the galaxy-dist/database/tmp could be removed manually. Also, I ran into this error when I was purging my deleted datasets: Error attempting to purge data file: /home/applications/galaxy-dist/database/files/000/dataset_89.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType' What does that mean? I am new to Galaxy and to python, so I was a bit confused after seeing this error. The purging went on fine, though. The datasets have been removed from the database. Cheers, CL

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Spaces in uploaded dataset filenames
by Oleksandr Moskalenko 19 Apr '12

19 Apr '12

Hi, I have a problem with a tool wrapper I wrote handling input files with spaces in their names. If a user uploads a dataset that has spaces in the file name, e.g. "foo bar.xml" file then even though my tool, which uses the last "tmp directory" method of handling multiple output files is provided by galaxy with a normal input filename like "/galaxy/production/database/files/006/dataset_6667.dat" the galaxy renames the output files to names based on the metadata like "foo bar.log" and "foo bar.nxs" output files, which don't get copied into the history. I wonder if anyone ran into this issue before and how it was handled. Thanks, Alex

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cleanup_datasets.py inquiry
by Ciara Ledero 19 Apr '12

19 Apr '12

Hi all, I have tried Nate's fix on this script, but I got an indentation error in line 31. Any ideas on how to fix this? I'm not familiar with python, so I'm quite at a loss here. Thanks!

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Manually deleting datasets from server
by Ciara Ledero 19 Apr '12

19 Apr '12

Dear all, I was able to execute the cleanup scripts in galaxy, using the -r option with them. According to what I've read, that option removes the datasets from the disk. But why didn't that happen? Also, since I have 'deleted and purged' the files, can I now remove them manually from the server? Cheers, CLedero

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Manually removing datasets from database
by Ciara Ledero 19 Apr '12

19 Apr '12

Dear all, I was able to run the cleanup scripts in Galaxy, using the -r option with them. But why weren't the datasets removed from the disk? Can I now manually remove them? Cheers, Diana M.

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Mira-Assembler: DOESN'T WORK ON GALAXY
by JIE CHEN 19 Apr '12

19 Apr '12

Dear all, I just installed Mira-Assembler via Galaxy tool sheds. As expected, it downloaded the wrappers into the "shed-tools" directory. Then I downloaded and installed Mira binaries on the system and add it to $PATH. Right now, mira can run successfully in the command line prompt. However when i run it in the Galaxy UI, i run into the below error: Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat SOLEXA_SETTINGS -LR:lsd=1:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 Anyone know why? Thanks in advance. Tyler

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Re: [galaxy-dev] Toolshed initial upload errors
by Paul-Michael Agapow 19 Apr '12

19 Apr '12

[For those who came in late - I've installed a local toolshed, which allows me to create repositories, but every time I attempt to upload files, it errors out with "TypeError: array item must be char". For those who come after me, here's what I worked out thus far.] Greg asked: > Since you've tried uploading various files with no success, the problem is likely > to be caused by something specific to your environment - possibly the version of > the mercurial package you're using. What version of Python are you running, and > what version of the mercurial package do you have installed with it? Also, what > version of Galaxy do you have, and what database / version are you using? We're CentOS, an older flavour (4), but my Mercurial is up to data (2.1.2). Python 2.6.4, Galaxy is 6799:40f1816d6857 (grabbed it fresh last week for testing), running it with sqlite. However, the Mercurial is actually installed local to the account I'm using, so I wonder if the toolshed is getting confused with another version, although hg doesn't seem to be installed on the system. Further investigations reveal that the files appear to be in the repo (database/community_files). The error manifest in the middle of Mercurial, in manifest.py where it attempts to coerce a Unicode string into a character array. (As there are some reported issues of Windows file names with Unicode under Mercurial, and I'm uploading from a Windows machine, I used a Mac to create a repo and add a file. Nope, same behaviour.) The Cistrome galaxy fork (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy…) mentions occasional similar errors. I check the Mercurial installation: % hg --version Mercurial Distributed SCM (version 2.1.2+10-4d875bb546dc) ... % hg debuginstall Checking encoding (UTF-8)... Checking installed modules (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial)... Checking templates (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial/templates)... Checking commit editor... Checking username... No problems detected (Actually, I was missing a username and a user ~/.hgrc file. But making that, it passes. Error still persists.) Work continues. ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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Re: [galaxy-dev] Potential database corruption with local galaxy instance
by Jeremy Goecks 19 Apr '12

19 Apr '12

>> % sh manage_db.sh downgrade 92 >> % sh manage_db.sh upgrade > The downgrade to 92 and upgrade created job.params. This is progress. You should be able to run jobs again, yes? > Unfortunately, we are still getting errors about duplicate key values. The debug output when I try to export a history to a file is shown below my signature. Is there anything that was updated recently that would change primary keys? Primary keys are handled by SQLAlchemy, not Galaxy, so that's not the problem. I would guess the issue arose due to the missing 'params' column in job. This can likely be fixed by deleting all the rows in the job_history_export_table: DELETE FROM job_export_history_archive; The only downside to this operation is that existing history archives won't be found and will have to be recreated. Best, J.

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Re: [galaxy-dev] linking Galaxy and Integrated Genome Browser
by Jeremy Goecks 19 Apr '12

19 Apr '12

Hiral, I've cc'd the Galaxy development mailing list, which includes folks with experience in all areas of Galaxy. Can you be clear about what you're trying to do and what approach you're taking? Once it's clear what the issue is, someone can chime in with suggestions. Best, J. On Apr 19, 2012, at 12:44 PM, Hiral Vora wrote: > Hi Jeremy, > > I have a question regarding committing my changes. > I need to make changes to datatypes_conf.xml. But I see that repository does not have that file. So should I commit my changes to datatypes_conf.xml.sample instead? > > Thanks, > Hiral

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Re: [galaxy-dev] How to specify RUM output dir?
by Dorset, Daniel C 19 Apr '12

19 Apr '12

Thanks Jeremy, that's very helpful, and it's great to hear from a developer! I have been pursuing option (a), and I feel like I'm very close. The RUM tool runs, and the filesizes show up in the history, but the datasets show up as erroneous. When I click on the apparently-problematic dataset's bug icon, the error message shows the following two lines repeated over 100 times: yes: standard output: Broken pip yes: write error I know what this means, generally, but not in the context of Galaxy. Is this a telltale symptom, or is it too generic to say? Under the additional output, it shows exactly the STDOUT the tool shows when it executes and terminates properly from the command line. So I know I'm close, I feel like I'm missing something small. When I click on the "view dataset button," I see the data, and it's legit. When I click "Edit Attributes," I see a message at the bottom of the "Edit Attributes" pane that says " Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values." When I attempt to run the Auto-detect, this notification goes away. It seems like the only issue right now is getting rid of that "broken pipe" error message. Once that's gone, perhaps the datasets won't be flagged as erroneous and I can use them in downstream processes. If I can get this tool working perfectly, I'll definitely upload it to the Galaxy toolshed. Any tips you could provide would be greatly appreciated! Thanks, Dan >You have two options: > >(a) you can set up the tool to report only a subset of outputs from the tool; > >or > >(b) you can use a composite datatype to store the complete directory: > >http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes > >Best, >J.

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