March 2014 - galaxy-dev - lists.galaxyproject.org

registration problem
by Wesley Schaal 22 Apr '14

22 Apr '14

Galaxy-Dev, I have a new galaxy installation under Linux. It's running as an Apache proxy (subdirectory) with authentication through galaxy (not apache). When trying to register a new user (which will be the administrator), the registration page declare success ("Now logged in as foo") but I am still just an anonymous user. If I try to login, it appears to succeed but I'm still anonymous. If I purposely enter the wrong password, the system complains as it should but I never get proper credentials. If I take away the Apache proxy configuration and run on the internal server, the problem goes away: I can login as expected and get the correct environment. The error is clearly here but I feel like I've followed the procedure written on the wiki. Specifically, Apache ----------- RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://localhost:8082$1 [P] # 8080 and 8081 are busy Galaxy --------- [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy Any idea of what might be wrong? Don't know if it matters but I'm using a MySQL database. I can see new users and it seems to work well enough to complain when bad passwords are entered. -- Wes

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(OperationalError) no such column: history_dataset_association.extended_metadata_id
by Peter Cock 22 Apr '14

22 Apr '14

Hi all, Earlier today I updated my development server, which uses SQLite, and ran the update schema script (now at v118). With hindsight there could have been a warning that I missed - because afterwards despite updating to the galaxy-central tip, trying to use any of the tools failed with an SQL error: OperationalError: (OperationalError) no such column: history_dataset_association.extended_metadata_id u'SELECT history_dataset_association.id AS history_dataset_association_id, ... $ ./manage_db.sh db_version 118 $ ./manage_db.sh version 118 Attempting a downgrade/upgrade suggested I had a stale migration_tmp table blocking this, Since this is only a development instance, I removed the SQLite database (and the old data files) to allow a clean regeneration: $ ./run.sh ... galaxy.model.migrate.check INFO 2014-02-18 13:25:52,248 Migrating 117 -> 118... galaxy.model.migrate.check INFO 2014-02-18 13:25:54,176 galaxy.model.migrate.check INFO 2014-02-18 13:25:54,177 Add link from history_dataset_association to the extended_metadata table galaxy.model.migrate.check INFO 2014-02-18 13:25:54,177 galaxy.model.migrate.check INFO 2014-02-18 13:25:54,177 migrate.versioning.repository DEBUG 2014-02-18 13:25:54,206 Loading repository lib/tool_shed/galaxy_install/migrate... ... This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Thanks, Peter

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read_bits64 error when loading large genomes/data into trackster
by Raj Ayyampalayam 16 Apr '14

16 Apr '14

Hello, I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10). When ever I try to do the above I see the following error in the logs: File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' Trackster works OK when I load smaller data sets. It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-…) How do I get the fixed code into my galaxy instance? Thanks, -Raj

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Jobs deleted staying in 'dr' status
by Mathieu Bahin 10 Apr '14

10 Apr '14

Hi all, We have been developing our own Galaxy instance for a while now. We have a cluster on which the job are sent to be executed, it is managed through SGE. Usually, communication between SGE and DRMAA is ok and we don't have any problem with that. When a job is deleted by the user, most of the times, the job disappears but sometimes, we don't know why, the job stays and has the status 'dr' within SGE. If we don't kill it 'manually', it stays forever. It is not always the same tools which produces this error . Have you any idea why how manage it ? We have another problem, a display one. Since the last update, we experienced problem with the history. Launching a job, it was very long to appear in the history and we had to refresh. We got a more recent version of firefox and it seems that we don't have the problem anymore. But some user of ours can't update their firefox. Are you aware of that problem ? Cheers, Genouest Platform, Rennes - FRANCE

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jobs stuck in new state
by David Hoover 09 Apr '14

09 Apr '14

I have many jobs stuck in the 'new' state on our local Galaxy instance. The jobs can't be stopped using the Admin->Manage jobs tool. First, does anyone know why a job would get stuck in the 'new' state for weeks? I have cleaned things up by manually setting their states to 'error' in the MySQL database. Is there a better way of dealing with 'new' jobs? BTW, our Galaxy instance was updated about two weeks ago. Wondering, David Hoover Helix Systems Staff

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extract_genomic_dna.py
by Adhemar 08 Apr '14

08 Apr '14

Hi, In order to have the transcript_id for each sequence extracted from the cuffmerge .gtf file I had to change the extract_genomic_dna.py by adding the following lines after line 153: attributes = gff_util.parse_gff_attributes( feature[8] ) if ( "transcript_id" in attributes ): name = attributes.get( "transcript_id", None ) This way the variable name gets the transcript_id if it exists. If it's correct, I would appreciate this modification in future galaxy distributions. Thanks! Adhemar

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Unable to remove old datasets
by Sanka, Ravi 07 Apr '14

07 Apr '14

Greetings, Despite being an admin, I am unable to remove old datasets from our Galaxy instance. I am following the procedure detailed in: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%2… 1. delete_userless_histories.sh 2. purge_histories.sh 3. purge_libraries.sh 4. purge_folders.sh 5. delete_datasets.sh --> desired to remove datasets before their outer container had been deleted 6. purge_datasets.sh None of the scripts have been changed. They all call cleanup_datasets.py with –d at 10 and –r enabled. But it does not appear to have any effect. All datasets (both those older than 10 days and those more recent) in <galaxy root>/database/files are still present, despite the –r setting in each script. Is there some parameter or such that needs to be set in the universe config that will allow this process to work? ---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------

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Galaxy packages for Bio-Linux - an update + Apache proxying
by Tim Booth 04 Apr '14

04 Apr '14

Hi All, As previously mentioned, I'm back working on packaging the Galaxy server as DEB packages for Bio-Linux (ie. Ubuntu 12.04 LTS) and ultimately pushing towards something that could be Debian compliant. There's a way to go in that regard, but I do now have an updated package for Bio-Linux in final testing and it also has a new trick: doing "apt-get install galaxy-server-apache-proxy" will set up just that with no further configuration needed. The galaxy server appears at http://localhost/galaxy and users log in with their regular system username and password. Uploads are enabled via regular SFTP so no special FTP server configuration is needed. It's a little hacky in parts but I'm generally pleased with the result. If anyone want to take a look I'd welcome comments. It's not in the main BL repo yet but can be found here: https://launchpad.net/~nebc/+archive/galaxy/+sourcepub/3711751/+listing-arc… Cheers, TIM -- Tim Booth <tbooth(a)ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705

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Better descriptions in job history?
by Smithies, Russell 04 Apr '14

04 Apr '14

Not sure if I've overlooked a setting somewhere, but is it possible to customize or tweak the job descriptions that are displayed in the history? Eg. "Compute sequence length on data 1" isn't very descriptive, but if perhaps the annotation field or a description field could be added it would make identification much easier eg. "Compute sequence length on data 1 [Burkholderia pseudomallei K96243]" or even for datatypes that have a defined definition line, perhaps a mouse-over hover could be added with the accession or definition pulled from the input file? These mouse-over hovers are already used to identify the view, edit, and delete icons so no additional libraries wold be used. I could probably hack something up but thought it better to try and get the feature included. Any thoughts? Thanx, --Russell

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(some) Tabular files not displaying correctly
by Lukasse, Pieter 04 Apr '14

04 Apr '14

Hi , I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine! Has anyone seen this before and what would be the solution/workaround? Screenshots: Bad: [cid:image002.jpg@01CF3932.37E5D170] Good: [cid:image003.jpg@01CF3932.37E5D170] Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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