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

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

1 0

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

2 2

Galaxy workflow editor cannot be loaded due to some JS files received 404 not found
by Derrick LIN 02 Oct '12

02 Oct '12

1 0

Orphan dataset created by history Export to File (possibly a bug?)
by Derrick Lin 01 Oct '12

01 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

4 6

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

8 10

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

2 1

October 2012 Galaxy Update
by Dave Clements 01 Oct '12

01 Oct '12

1 0

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

2 1

Size of the genome indexes repos in Galaxy Main
by Derrick Lin 01 Oct '12

01 Oct '12

Hi guys, Just a quick question about the total size of the genome indexes just made available via rsync server? Cheers, Derrick

2 4

markupsafe module conflicts
by Fenglou Mao 01 Oct '12

01 Oct '12

Galaxy imported a library which already existed in the python system folder. See the error message below. /home/xxxxx/work/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /home/xxxxx/work/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() The system package is python-markupsafe-0.9.2-4.el6.x86_64 Galaxy has a newer version, it is MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg Any idea how to resolve this problem? Thanks, Fenglou

2 1