April 2010 - galaxy-dev - lists.galaxyproject.org

Dynamically adding tools to Galaxy
by Sumedha Ganjoo 26 Jul '10

26 Jul '10

Hello, I am a student at the University Of Georgia. We had developed a tool for Galaxy 1.3 that enables accessing various web services as tools from Galaxy. We are currently working on a similar tool for the current version of Galaxy. This requires adding a tool dynamically without having to restart Galaxy. I was wondering if someone has already implemented that feature? We do have most of the code for this in place. Is there a way, once complete, this code can be added to the main Galaxy source code? Also I would really appreciate if someone could tell me where can I find the older versions ( v 1.3 ) of Galaxy? Thanks in advance. Regards, Sumedha Sumedha Ganjoo Graduate Assistant Computer Science Department University Of Georgia

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Re: [galaxy-dev] [galaxy-user] MACS input format
by Steve Taylor 05 May '10

05 May '10

On 30/04/2010 15:37, Daniel Blankenberg wrote: > Hi Steve, > > The latest version in the repository and on the test server accepts bed, sam, bam, eland and elandmulti for single-end and elandmulti only for paired-end. The version currently on the main public server accepts bed, sam, and bam for single-end with paired-end not functioning. The newest version of MACs will be available on the main public server the next time it is updated. > > Strange. On our local Galaxy instance I got ERROR:root:Format "SAM" cannot be recognized! and the bowtie (SAM) format was generated from within Galaxy. Any ideas why? Steve

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Asking for Galaxy main public instance support, thanks!
by WangJun 04 May '10

04 May '10

Hello Dr Greg Von Kuster, We are developing a Rice Genome Browser: Rice-Map. I am writing to ask if you can add our resource to your main public instance so that users can get data from Rice-Map and do analysis in your platform conveniently. Steps for adding Rice-Map: 1. Add tool definition file "cbi_rmap_browser.xml" under tools/data_source directory (attached). 2. Add this tool into file "tool_conf.xml" in the "Get Data" section: <tool file="data_source/cbi_rmap_browser.xml" /> Thank you in advance! Best wishes, Kathleen Center for Bioinformatics Peking University

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Galaxy issue
by Modi, Amit 02 May '10

02 May '10

Hi, We are trying to configure Galaxy to work with our tool. So far I have been able to configure it well and link it with the cluster to do process all the jobs as per the documentation . Now what we want is the before the actual processing starts the validations for the input files are done on the Local. And the job processing is done on the cluster. Is there anyway we can configure this. We are using sge on the cluster. Thanks a lot. Regards, Amit Modi ----------------------------------------- Confidentiality Notice: The following mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. The recipient is responsible to maintain the confidentiality of this information and to use the information only for authorized purposes. If you are not the intended recipient (or authorized to receive information for the intended recipient), you are hereby notified that any review, use, disclosure, distribution, copying, printing, or action taken in reliance on the contents of this e-mail is strictly prohibited. If you have received this communication in error, please notify us immediately by reply e-mail and destroy all copies of the original message. Thank you.

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tiny usability issue - cloning vs. importing shared history
by Assaf Gordon 02 May '10

02 May '10

Hi, I've noticed a small usability annoyance with shared histories. Scenario: A user shared a history with me. The new history appears in the "Histories shared with you by others" page. I click on the history name, get a popup menu with three options: View, Clone, Unshare. If I choose "clone", the history is cloned and appears in my "saved history". If I choose "view" (and look at the library) then click on the green import button, I get a red error message: "The owner of this history has disabled imports via this link. You can return to the previous page." I understand that "cloning" is technically different from "import via link", but conceptually, the end result is the same - I should get the shared history into my histories. So it's quite confusing when I get this error message. Since I'm slightly familiar with Galaxy, I realized that the correct thing to do is go back to the list of shared-histories, then "clone" instead of import. An inexperienced user might think that something is wrong with the sharing. Somewhat related: After importing a history via link, the "start using this history" link does not work if the current history a non-empty. To reproduce: 1. go to http://main.g2.bx.psu.edu/ 2. click "options" -> "create new". 3. current history is empty. 4. go to http://main.g2.bx.psu.edu/history/list_published 5. select any one of the histories (e.g. "SM_1186088") 6. Click on the green plus button to import the history. 7. The following message is displayed: History "imported: SM_1186088" has been imported. You can start using this history or return to the previous page. 8. click on "start using this history", you'll be back on the main galaxy web site, with this new history selected. So far, so good. Now, repeat steps 1-8, but instead of creating a new, empty history (step 2,3), select a non-empty history or upload some dummy data set. After clicking "start using this history" (step 8) you'll be at the *old* history, not the newly imported one. -gordon

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grouping and sorting error at a bare local installation
by Jordi Rambla 02 May '10

02 May '10

Hi, I'm quite new to Galaxy and Python, but I have near 25 years of experience at computing (development, databases, web development, systems.) I've performed a local installation in order to learn Galaxy and it's "internals". In order to test the installation, I'm reproducing the Galaxy screencast tutorials locally. When reproducing the screencast named : "Finding Exons with the highest number of nucleotide polymorphisms", at step 4 (grouping and counting). I'm receiving the following error: "An error occurred running this job: Sorting input dataset resulted in error: 512: sort: multi-character tab `$\t'". Just to doublecheck, I've tried to just sort the dataset on column 4 (Name), and I'm receiving a quite similar error ("An error occurred running this job: sort: multi-character tab `$\t'"). I've tried to locate the error source at the configuration/ source code files. but found nothing promising on filters/sorter.py nor stats/grouping.py. Thus, I'm asking for a tip on where to look at. Thanks in advance. Jordi Rambla Universitat de Barcelona

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data visualization in galaxy trackster
by Vipin TS 30 Apr '10

30 Apr '10

Hi Galaxy team, I am trying to visualize data in galaxy using trackster. I made necessary requirement based on the documentation in http://bitbucket.org/galaxy/galaxy-central/wiki/Visualization. My data set in wiggle variableStep format. below here is few lines from my wiggle file track type=wiggle_0 name="test run" variableStep chrom=III 1841 1 1842 1 1843 1 1844 1 1845 1 1846 1 1847 1 1848 1 1849 1 1850 1 1851 1 1852 1 1853 1 It is about 3.2MB in size and I tried to create a new track browser in my local galaxy instance. Unfortunately it just shows the message "Loading data ..." for the last five hours. Any ideas are sincerely appreciated. many thanks, Vipin T S

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Error for one user when using edit properties
by SHAUN WEBB 30 Apr '10

30 Apr '10

Hi, we are having problems with a single user account. When using the 'edit attributes' button on a dataset an error is returned (traceback below). This is happening with each dataset/history. However, if the dataset is shared then properties can be edited by a different user or while logged out. It appears to be solely linked to this users account. Thanks in advance for any help. Shaun Webb When trying to 'Edit Attributes' URL: http://bifx3.bio.ed.ac.uk:8080/root/edit?id=2558 File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/opt/galaxy_dist/lib/galaxy/web/controllers/root.py', line 364 in edit all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' ) File '/opt/galaxy_dist/lib/galaxy/security/__init__.py', line 174 in get_legitimate_roles return sort_by_attr( [ role for role in roles ], 'name' ) File '/opt/galaxy_dist/lib/galaxy/security/__init__.py', line 142 in sort_by_attr intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) AttributeError: 'NoneType' object has no attribute 'name' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Job Control in Galaxy
by Steve Taylor 30 Apr '10

30 Apr '10

Hi, We have configured our Galaxy system to use Sun Grid Engine in shared mode. We noticed that on submission of a job that running qstat does not show the jobs status. It looks the a wrapper shell script defining the environment and the command(s) is being submitted and then as far as SGE is concerned the job is done (however, the job is still running on the application server). I don't understand when using this system how you can manage submitted jobs. Isn't the point of using a queuing system like SGE that you can manage the load on the servers using the SGE configuration tool (qconf) to control the queues? Or am I misunderstanding something? Thanks for any advice, Steve

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Re: [galaxy-dev] NGS peak calling: MACS
by Vipin TS 30 Apr '10

30 Apr '10

Hi Kanwei, I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1 each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score. thnaks, Vipin T S On 27 April 2010 19:17, Kanwei Li <kanwei(a)gmail.com> wrote: > Hi Vipin, > > What is a bed wiggle file? We support both, but not at the same time :P > > Kanwei >

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