- galaxy-dev - lists.galaxyproject.org

submitting jobs as the real user
by David Hoover 02 Oct '12

02 Oct '12

I'm playing with the "submitting jobs as the real user" method, and immediately ran into a problem. Uploaded files are created in mode 600, owned by the user. Galaxy then gives an error that the tmp file is not readable: IOError: [Errno 13] Permission denied: '/spin1/users/galaxy/galaxy2/database/tmp/tmp3KHIDt' Is there any way of changing the permissions on the temporary uploaded file to 666? David Hoover Helix Systems Staff

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Error when running cleanup_datasets.py
by Liisa Koski 02 Oct '12

02 Oct '12

Hello, I am trying to run the cleanup scripts on my local installation but get stuck when trying to run the following: ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r Deleting library dataset id 7225 Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders _purge_folder( folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 495, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) AttributeError: 'NoneType' object has no attribute 'id' Any help would be much appreciated. Thanks, Liisa

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Trouble setting admin status and uploading files
by Jackie Lighten 02 Oct '12

02 Oct '12

Hi All, I installed a local Galay instance but found uploads to be incredible slow. I have seen this can be remedied through Admin controls. However my modifications to "universe_wsgi.ini" still do not enable me to log in as Admin showing the following error message: "No such user " I edited universe_wsgi.ini as follows: 1. ### Admin Users admin_users = my email address I closed Galaxy and re-launched with the modified file, however still no login ability. I am running this on a desktop, no network. Any help would be appreciated. Cheers, Jack

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LDAP integration and migration of users
by Joachim Jacob 02 Oct '12

02 Oct '12

Hi all, I wonder if somebody with experience could enlighten me on these issues regarding authentication of users. - is it possible to have LDAP integration simultaneously with local Galaxy users. What I want to reach is when LDAP integration is working, that I can still add users through the Galaxy admin interface (users that are not present in the LDAP). - is there a way to transfer all histories, workflows and visualisation to another user? For example, an existing user receives a new email and password, and want to transfer all his/her stuff to this new account. Can this be done? I was thinking about when a user gets transferred to the LDAP, he/she would be able to transfer all data from the old account to the new account. Thanks, 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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Galaxy workflow editor cannot be loaded due to some JS files received 404 not found
by Derrick LIN 02 Oct '12

02 Oct '12

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Orphan dataset created by history Export to File (possibly a bug?)
by Derrick Lin 02 Oct '12

02 Oct '12

hi guys, I have been trying to clean up some old histories and datasets on our local galaxy. I have spotted one very old dataset file with big size didn't get removed no matter what. I went to check the reports webapp, that dataset isn't on the largest unpurged data files list (despite it has bigger size). Then I moved on to checking the database, no history or library associates with that dataset. Finally, I found its trace in job_to_input_dataset, so I could identified the job id and found that it's the file created by history Export to File. I also find relevant entry in job_export_history_archive. Since such datasets are not associated with any history, library, the documented dataset cleanup method does not work on them. Any suggestion? Regards, Derrick

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How to rotate Galaxy log file
by Jennifer Jackson 01 Oct '12

01 Oct '12

repost to galaxy-dev On 9/7/12 6:39 PM, Lukasz Lacinski wrote: > Dear All, > > I use an init script that comes with Galaxy in the contrib/ subdirectory > to start Galaxy. The log file > > --log-file /home/galaxy/galaxy.log > > specified in the script grows really quickly. How to logrotate the file? > > Thanks, > Lukasz > ___________________________________________________________ > 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/ -- Jennifer Jackson http://galaxyproject.org

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Jeremy's DataProvider changes
by Ted Goldstein 01 Oct '12

01 Oct '12

I just saw the new Data Provider changes. Is still looks very focused on genomic data needed by Trackster. I would like to have a general mechanism for generating heatmaps for systems biology. We need similar separation of data and presentation. Should we consider the new API? Thanks Ted http://soe.ucsc.edu/~ted

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October 2012 Galaxy Update
by Dave Clements 01 Oct '12

01 Oct '12

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speed and large file question (after tying galaxy to Pittsburgh)
by Joseph Hargitai 01 Oct '12

01 Oct '12

Hi, General: Is there a quantifiable difference in data uploads, speed of processing, general availability after the connection was/is established to Pittsburgh? Specific: If we loaded data to a common directory on an XSEDE resource, would our students be able to fetch this data in a more timely manner to their galaxy accounts then from desktops etc... For us it would be easy to populate a common directory once then our users could fetch/wget etc... from there, or if possible could such directory be directly visible to our set of galaxy users? (this is what we do locally) - but one would need admin priv for that on the main instance. Or would you just do this with one galaxy user sharing out the files for the rest of a group working together? thanks. joe

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