- galaxy-dev - lists.galaxyproject.org

character set encoding metadata
by Robert Baertsch 29 Nov '13

29 Nov '13

Does galaxy have an official place to store the character set for a text file? I'm thinking of modifying the upload tool to prompt for the character set, since it cannot be sniffed. It should go in the hda/ldda metadata hash or extended_metadata for the dataset. Any opinions? BTW: everyone should watch this talk on unicode. http://bit.ly/unipain

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Re: [galaxy-dev] galaxy-dev Digest, Vol 89, Issue 32
by Dooley, Damion 28 Nov '13

28 Nov '13

Hi folks, Has someone seen this behaviour? I'm trying to do a once-over maintenance cleanup of our galaxy installs. The galaxy account is getting emailed nightly with an error which is happening when it gets to delete_datasets.sh cron task, basically: AttributeError: 'NoneType' object has no attribute 'dataset_id' 1) Now I found this thread: http://dev.list.galaxyproject.org/Error-when-running-cleanup-datasets-py-td… - and implemented that solution which removed some of the preceding log error info, but this related error remains: sh ... /production2/galaxy-dist/scripts/cleanup_datasets/delete_datasets.sh 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 126, in main delete_datasets( 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 301, in delete_datasets dataset_ids.append( ldda.dataset_id ) AttributeError: 'NoneType' object has no attribute 'dataset_id' In the delete_datasets.log it shows that this is last log line before error occurs: ######### Processing LibraryDataset id: 14201 2) So to recap, in step 1 I found: galaxydb_prod2=> select * from library_dataset where library_dataset_dataset_association_id is null; id | library_dataset_dataset_association_id | folder_id | order_id | create_time | update_time | name | info | deleted | purged -------+----------------------------------------+-----------+----------+----------------------------+----------------------------+---------------+------+---------+-------- 14201 | | 544 | 18 | 2012-11-01 17:26:23.877817 | 2012-11-01 17:26:35.787611 | NC_006625.fna | | f | f (1 row) And so I ran the recommended query, "update library_dataset set folder_id = null where id=14201;" and that seemed to have a positive effect. For what its worth, galaxydb_prod2=> select * from library_dataset_dataset_association where id = 14201 galaxydb_prod2-> ; id | library_dataset_id | dataset_id | create_time | update_time | copied_from_history_dataset_association_id | copied_from_library_dataset_dataset_association_id | name | info | blurb | peek | extension | metadata | parent_id | designation | deleted | visible | user_id | message | state | tool_version -------+--------------------+------------+----------------------------+--------------------------+--------------------------------------------+----------------------------------------------------+---------------+------+-------+------+-----------+------------------+-----------+-------------+---------+---------+---------+---------+-------+-------------- 14201 | 14201 | 14706 | 2012-11-01 17:26:28.593081 | 2012-11-01 17:26:30.8649 | | | NC_006625.fna | | | | auto | {"dbkey": ["?"]} | | | f | t | 1 | | | (1 row) The last thing I'd say is that this 'NC_006625.fna' item doesn't show up in the website front-end's sole Data Library list of folders and sub-items, nor does it show in the deleted list. It seems orphaned but I'd rather someone had confident advice on this one. My novice attempt at surgery would probably lead to lots of blood on the table. Help much appreciated! Damion

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Active Directory
by Alexander Kurze 28 Nov '13

28 Nov '13

Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive?

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Active Directory
by Alexander Kurze 28 Nov '13

28 Nov '13

Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? Alex

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Active Directory
by Alexander Kurze 28 Nov '13

28 Nov '13

Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? Alex -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865

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Uploading files from password protected URL's
by Nicolas Cybulski 28 Nov '13

28 Nov '13

Thanks a lot for the answer ! kind regards, Nicolas Cybulski

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Add a tool to galaxy
by sun liang 28 Nov '13

28 Nov '13

hello all, We have a transcript classification tool named CNCI, that published on NAR August 6 2013, and the title of this article is "Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts". The source code is writen by python, and can be download at : http://www.bioinfo.org/software/cnci/ . We would like to add CNCI to galaxy cloudman, and help more researchers in transcriptome analysis community . If have any question please contact me! Looking forward to hearing from you soon. Yours sincerely,

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Dynamic tool loading
by Mikel Egaña Aranguren 28 Nov '13

28 Nov '13

Hi; I have developed a tool generator that performs a SPARQL query (defined by the user) and creates new Galaxy tools depending on result. I have the basic system (i.e. it generates the tool XML files and edits the tool_conf.xml in the "traditional" way) but I would like my tool generator to be a regular Galaxy tool that is able to "inject" the new tools in the Galaxy menu without having to restart Galaxy. Is there an easy way of doing so? I have come across this thread ( http://osdir.com/ml/galaxy-development-source-control/2010-07/msg00094.html) but it is not clear for me: - If this change has been implemented in Galaxy. - If it has been implemented, what should be the output of my tool generator. Thanks Regards -- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com

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Library permission page broken
by David Hoover 28 Nov '13

28 Nov '13

After the latest update, the "Manage library permissions" page is broken. The "Roles not associated" boxes are pushed to the left of the frame, and the double arrow buttons are misplaced down the page. This occurs under Safari (5.1.10) and Chrome (31.0.1650.57) on a Mac running OS X 10.6.8. Firefox (25.0.1), however, seems ok.

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Uploading files from password protected URL's
by Nicolas Cybulski 27 Nov '13

27 Nov '13

Hi all, I am trying to upload data from a password protected website (http://ddlab.sci.univr.it/~centrogenomica/huang_no_project/) My stdout is (obviously0 "Enter username for Reserved Area at ddlab.sci.univr.it:") which is kind of normal but not what I wont of course. Is there a way around this problem ? Kind regards, Nicolas Cybulski Galaxy application manager VIB - PSB Gent

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