April 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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double check for "EMS Variant Density Mapping"
by Wang, Xiaofei 22 Apr '14

22 Apr '14

Dear folks, Could you help me double check if my understanding is correct for EMS density mapping? For the tool "CloudMap: EMS Variant Density Mapping", it does not work for other species except C.elegans, correct? For the workflow "CloudMap EMS Variant Density Mapping workflow (takes VCF of heterozygous and homozygous variants to subtract)" in published workflows, the final step is to plot the VCF output using the tool "CloudMap: EMS Variant Density Mapping". If I want to use this workflow on other species, I need to remove this tool/step from the workflow by edit it. If I do not remove this step, there is nothing in the output of "EMS Variant Density plot" even the color is green for this step in the history, right? Thanks a lot! Best, Xiaofei

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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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Re: [galaxy-dev] automatically adding fasta files to "built-in" databases and selecting files questions
by Hans-Rudolf Hotz 22 Apr '14

22 Apr '14

Hi Nik Have a look at the "Profile Annotations" tool (~/tools/annotation_profiler/annotation_profiler.xml) and the file ~/tool-data/annotation_profiler_options.xml Regards, Hans-Rudolf On 04/19/2014 12:48 AM, Nikhil Joshi wrote: > Hi Hans, > > Thanks for your response. I am trying to get just one part working right > now, and that is the selecting of a database file. You suggest using a > drill_down, but I can't seem to find good documentation on how to get it > to work. I have been looking at the annotation_profiler tool to get > ideas, but it still is unclear to me. Can you give me a simple example > of how one would create the file that the drill_down would use and then > how to use that file? > > - Nik. > > > > On Wed, Apr 9, 2014 at 1:13 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Nik > > I don't think there is a solution out of the box for all of this, > but I will try to give you some pointers - others might have > different or even better suggestions (my suggestion are very > 'hacky'). Let me answer your questions in reverse order: > > - Instead of using "Add another file", display all your files as > checkboxes: > > type="select" display="checkboxes" multiple="true" > > you then get a comma separated string with containing all the > selected files > > one option to populate the checkboxes is using "dynamic_options" or > "from_file" which both allow you to read the list of files stored in > a extra table > > > - A list with thousands of files to choose from is obviously not very > handy. You can build a tree where you can open and collapse > individual branches using > > type="drill_down" together with "from_file" > > Or as an alternative to searching, you can use "conditional" and then > only display part of the list. > > > - you can write a little tool, which allows people to select a > history item (or uploads a new file) which is then stored at a new > location (outside the galaxy database directory). In a second step, > this tool adds the item to the table which is read by > "dynamic_options" or "from_file". Using "from_file" would require a > restart, but a tool reload. > > > I hope you get a few ideas out of this > > Regards, Hans-Rudolf > > > > > On 04/09/2014 04:34 AM, Nikhil Joshi wrote: > > Hi all, > > We have a local install of Galaxy that we use for testing for our > bioinformatics courses. I am creating some new tool interfaces > for the > install. I want to create a tool that will allow a user to > automatically > add a fasta database to the "built-in" databases (without needing to > reboot the server). Is this possible? > > Along with that issue is that the number of databases for this > tool can > number in the thousands. Is there a way to easily search the > built-in > databases for the database you are looking for, and then use that > database in a tool? Right now, it is an enormous drop down list > which is > really annoying and unwieldy. > > Finally, these tools can take multiple input files, but I really > don't > like the way galaxy handles that where you have to continually > click on > "Add another file". Is there a method or work-around in galaxy > where you > can have a multi-file select? > > - Nik. > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.__edu/ > <http://bioinformatics.ucdavis.edu/> > najoshi -at- ucdavis -dot- edu > 530.752.2698 <tel:530.752.2698> (w) > > > _____________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/__search/mailinglists/ > <http://galaxyproject.org/search/mailinglists/> > > > > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > najoshi -at- ucdavis -dot- edu > 530.752.2698 (w)

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Re: [galaxy-dev] Migrate user data to a new server
by Derek Benson 21 Apr '14

21 Apr '14

Hi Simon I too have been down the long and fruitless task of searching for details about how to migrate a public (or not so public) galaxy server to a completely new host. In the end, I made some assumptions, strapped on my jodhpurs and spurs and dived in. Now I don't know whether what I've done is supported or encouraged by the galaxy team, or if its even the right way of doing this but after completing the steps below I was met with great success. 0. Assume that there is an old server running galaxy, and a brand new server running galaxy. 1. Stop Galaxy processes and Postgresql databases on old and new server. 2. To get the user data rsync /mnt/galaxy/files from old server to new server (assuming your galaxy instance is under /mnt/galaxy) 3. To get the database: a) remove the directory /mnt/galaxy/db on the new server (again assuming /mnt/galaxy is the path to your galaxy instance) b) Rsync the database files from the old server's /mnt/galaxy/db to the new server. 5. Update the database on the new server. I'm using cloudman to run a virtual instance of a galaxy server, and so I used cloudman to update the database. a) Attempt to start galaxy through cloudman (in my case this failed if I waited too long) b) Wait a second or 2, and then ask cloudman to update the database (this shutsdown galaxy and updates the database and then restarts galaxy). There is a command line script you can run that comes with galaxy and which can be used to update the database manually. If you attempt to start the galaxy process and the database is an older version the log files will contain a message about how to run this. You're done. Derek PS. Apologies for the terrible formatting in this Email. -- Systems Administrator Cloud Computing Genomics Virtual Lab Reseach Computing Centre The University of Queensland 4072 Australia Phone: +61-7-33462276 Fax: +61-7-33466630 Mobile: 0411 145 379 Email: d.benson(a)uq.edu.au Web: http://www.rcc.uq.edu.au

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FW: uploading data libraries options
by mark.rose＠syngenta.com 21 Apr '14

21 Apr '14

Nevermind, I found it in universe_wsgi.ini. Mark From: Rose Mark USRE Sent: Monday, April 21, 2014 10:09 PM To: galaxy-dev Subject: uploading data libraries options Hello when attempting to create data libraries as admin I am not presented with the same options listed in the documentation, namely [cid:image001.png@01CF5DAE.5B451360] Instead I only get "Upload Files" and "Import datasets from your current history". I want to use "Upload files from filesystem paths". What should I do? Thanks Mark ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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uploading data libraries options
by mark.rose＠syngenta.com 21 Apr '14

21 Apr '14

Hello when attempting to create data libraries as admin I am not presented with the same options listed in the documentation, namely [cid:image001.png@01CF5DAE.5B451360] Instead I only get "Upload Files" and "Import datasets from your current history". I want to use "Upload files from filesystem paths". What should I do? Thanks Mark ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Huttenhower Galaxy bug
by Erin McKenney 21 Apr '14

21 Apr '14

Hello, I am trying to use LEfSe (on the Huttenhower Galaxy instance) to analyze the data table attached. I formatted the table according to LEfSe guidelines, but the table cannot be formatted after it is loaded to Galaxy. I also tried formatting a table that was successfully analyzed on the Huttenhower instance a year ago. That (previously successful) table cannot be formatted either. I suspect that there is a bug. Can you please help me to resolve the bug or tell me an alternative way to analyze the data? Thanks, Erin

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GCC2014 Poster Abstracts due April 25, THIS FRIDAY
by Dave Clements 21 Apr '14

21 Apr '14

Hello all, This is just a reminder that poster abstracts for the 2014 Galaxy Community Conference (GCC2014) *are due this Friday. * Abstracts can be submitted at https://wiki.galaxyproject.org/Events/GCC2014/Abstracts Note that posters are reviewed and accepted on a rolling basis, until all slots are full. The deadline is this Friday but sooner may be better. In other news: - We are delighted to have Steven Salzberg as the keynote speaker<https://wiki.galaxyproject.org/Events/GCC2014#Keynote_Speaker> . - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon>is now open - Early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register>for the GCC2014 Training Day and Meeting<https://wiki.galaxyproject.org/Events/GCC2014/Program>are also open - Abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>for accepted talks will start showing up on the website this week. Thanks, and hope to see you in Baltimore, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > *We are pleased to announce that Early Registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and > Poster Abstract Submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for > the 2014 Galaxy Community Conference (GCC2014) > <https://wiki.galaxyproject.org/Events/GCC2014>.* > > GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at > the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns > Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, > United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring > four *five* parallel tracks, each with three, two and half hour long > workshops. There are 13 different topics spanning the full Galactic > spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> > > *Early registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. > Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main > meeting) starting at $140 for post-docs and students. Registration is > capped this year at 250 participants, *and we expect to hit that limit*. > Registering early assures you a place at the conference and also a spot in > the Training Day workshops you want to attend. > > You can also book affordable conference housing at the same time you > register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. > > *Abstract submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral > presentations and posters is also open. Abstract submission for oral > presentations closes April 4, while poster submission closes April 25. > Poster authors will be notified of acceptance status within two weeks of > submission, while presentation authors will be notified no later than May2. > *Please consider presenting your work. If you are dealing with big > biological data, then this meeting wants to hear about your work.* > > The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data > Intensive and Reproducible Research" series announced for the last > conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, > *and is continuing to take submissions for this year's meeting and beyond*. > BGI is also continuing to cover the article processing charges until the > end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. > > > Thanks, and hope to see you in Baltimore! > > The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Trackster : Error visualising VCF
by Saket Choudhary 21 Apr '14

21 Apr '14

I am trying to visualise VCF exported from: ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz However I get the following error: (Both on Galaxy Main and Local installation) Input error: Chromosome 1 found in your input file but not in your genome file. needLargeMem: trying to allocate 0 bytes (limit: 100000000000) The input file seems to be conforming to VCF4.1 format. Is this an issue with trackster instead? Saket

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