galaxy-dev October 2013

galaxy-dev@lists.galaxyproject.org

112 participants
166 discussions

Re: [galaxy-dev] Job splitting
by Bjoern Gruening 17 Oct '13

17 Oct '13

Hi Peter, > <bjoern.gruening(a)gmail.com> wrote: > > Hi Peter, > > > > I saw your are working again on the job splitting features. I may have a > > features request: > > Well, not really working on it - just reporting a regression using it. Ah ok :) > > For some tools you have different file formats as input but only for one > > or two of them the split and merge function are defined. If the filetype > > is now one of these non splittable ones, Galaxy will crash. I think a > > better way would be to default to non-split mode? > > I guess that isn't supported. > > > Does that make sense for you? Any pointer where to look? Its not urgent, > > but it was on my todo list. Just remembered it, reading your mail. > > Yes, that makes perfect sense. Possibly here lib/galaxy/jobs/__init__.py > it needs to look at the datatype to see that supports splitting: > > def can_split( self ): > # Should the job handler split this job up? > return self.app.config.use_tasked_jobs and self.tool.parallelism > > We could/should take this discussion to galaxy-dev, Sure, I thought it would be more easier, some missing "return" or something. Will have a deeper look at it if I have some more time. Trello card is here: https://trello.com/c/lIKKwiC1 Thanks! Bjoern > Regards, > > Peter

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Deploying LOC files for tool built-in data during a tool installation
by Jean-Frédéric Berthelot 17 Oct '13

17 Oct '13

Hi list, The tool I am currently wrapping has built-in data, which may be used by the tool users (through a relevant < from_data_table> + .LOC file configuration). They are .fasta databases which are rather small and are thus bundled in the tool distribution package. Thanks to the tool_dependencies.xml file, said distribution package is downloaded at install time, code is compiled, and since they are here, the data files are copied to $INSTAL L_DIR too , ready to be used. After that, the user still has to edit tool-data/my_fancy_data_files.loc ; but the thing is, during the install I know where these data files are (since I copied those there), so I would like to save the user the trouble and set up this file automagically. I would have two questions: 1/ Is it okay to have tool built-in data files in $INSTAL L_DIR, or would it be considered bad practice? 2/ Is there a way to set up the tool-data/my_fancy_data_files.loc during the install? Here are the options I though of: *shipping a “real” my_fancy_data_files.loc.sample with the good paths already set-up, which is going to be copied as the .loc file (a rather ugly hack) *using more <action type="shell_command"> during install to create my_fancy_data_files.loc (but deploying this file it is not part of the tool dependency install per se) *variant of the previous : shipping my_fancy_data_files.loc as part of the tool distribution package, and copy it through shell_command (same concern than above). Any thoughts? Cheers, -- Jean-Frédéric Bonsai Bioinformatics group

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Problem configuring Galaxy with an Apache proxy
by Erwan Delage 17 Oct '13

17 Oct '13

Hello everyone, I'm having trouble setting up Galaxy with an Apache Proxy. I did edit the Apache conf file with the following lines : RewriteEngine on RewriteRule ^/static/style/(.*)/home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*)/home/nate/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*)/home/nate/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico/home/nate/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt/home/nate/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] The redirection seems to "work" as I reach a webpage that contains some Galaxy's links but, as you can see in the attached snapshot, the webpage does not really looks like the usual Galaxy welcome page :) Did you already face that problem or do you have any idea to solve it ? Thanks, Erwan, -- Erwan Delage Ingénieur d'études - Equipe COMBI LINA - Université de Nantes Tel : 02 51 12 58 21

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bug in handling sessions
by Nikolai Vazov 17 Oct '13

17 Oct '13

Hi, I have discovered the following weird Galaxy behaviour. If one sets log_actions = True in universe_wsgi.ini and tries to display the Saved Histories, then the Saved histories don't show up. The problem arises from ../lib/galaxy/web/framework/helpers/grids.py line (around 230) trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params) Until this line, the Query object 'query' has queried the DB and fetched the necessary data. Yet, in the file ../lib/galaxy/web/framework/__init__.py in the function log_action self.sa_session.flush() seems to flush everything, including the data fetched by the 'query' object in grids.py Thus, the Saved Histories get "No Items" message. Commenting out the line log_actions = True does the job, but ... Any suggestions? Best regards Nikolay -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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Re: [galaxy-dev] Tabular data not displaying in main panel
by Ian Misner 17 Oct '13

17 Oct '13

Hello All, I'm having the same issue with tabular data not displaying,but I'm afraid I'm much newer to running a local galaxy instance. Apparently switching to https://bitbucket.org/galaxy/galaxy-central/src/a477486bf18eafdd14dd7ba1e91… but frankly I don't know how to do that. Any help would be appreciated. Here is my current branch information changeset: 10421:a477486bf18e branch: stable tag: tip user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 26 11:02:58 2013 -0400 summary: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. changeset: 10411:c42567f43aa7 user: greg date: Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. Cheers Ian

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random_lines_two_pass.py slow
by Ido Tamir 17 Oct '13

17 Oct '13

Hi, my users start to take comparability serious and start to downsample. But it seems like the random_lines_two_pass.py tool is very slow with large input files, like bed files with 40million reads to e.g. 33million reads https://bitbucket.org/galaxy/galaxy-dist/src/2469c53051ea/tools/filters/ran… I don't understand the rationale behind the deletion of the positions from the array, in most programming languages deletion from an array is slow. Benchmarking the two random sampling methods was too difficult for me, I removed the get_random_by_subtraction method, and my users are happy. Did anybody really benchmark this? thank you very much, ido

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Interact with running job?
by Jonas Hagberg 17 Oct '13

17 Oct '13

Hej I am new to Galaxy. I am reading the documentation but could not really find an answer . I would like to create a tool that when after executed on a cluster the user should be able to interact with the running job. Get the current output and make a plot and see how far the job has come. Clicking on special status link on the running job in history or something like that. How would one do this in galaxy. Is there any way today to do it with the tools in galaxy. Would be great to get some first guidance where to start. cheers -- Jonas Hagberg BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se e-mail: jonas.hagberg(a)bils.se, jonas.hagberg(a)scilifelab.se phone: +46-(0)70 6683869 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden

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Integrate Galaxy workflow as a tool in Galaxy
by shenwiyn 17 Oct '13

17 Oct '13

Hi Galaxy team, We find that Galaxy workflow is much more convenient and operable for biodata analysing.Now we get an idea about integrating our Galaxy workflow as a tool in Galaxy,such as RNAdenovo,Chip-seq,and so on.We do not know whether some other Galaxy try the same or not ,and whether it is necessary and feasible for our idea.Thank you for any suggestions. shenwiyn

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Apache and Galaxy
by UMD Bioinformatics 17 Oct '13

17 Oct '13

Hello, I have set up a galaxy instance and I'm trying to use Apache so that I can access UCSC. I have the following set in my httpd.conf (below) file in Apache2 and I've altered the folioing in my universe_wsgi.ini file. When I launch galaxy I no longer see my history. If it attempt to login the screen refreshes but it does not log me into the system. i.e. my history does not show up and I do not get the admin tab to appear. What am I doing wrong? httpd.conf settings #Changes for Galaxy 16 Oct 2013 # Define Galaxy as a valid Proxy <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> RewriteEngine on <Location "/"> XSendFile On XSendFilePath / </Location> RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/static/style/(.*) /Volumes/Jose-Drobo/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /Volumes/Jose-Drobo/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /Volumes/Jose-Drobo/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /Volumes/Jose-Drobo/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] #ucsc <Location "/root/display_as"> Satisfy Any Order deny,allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> <LocationMatch /ucsc_(bam|big) > # This is to enable bam and bigWig (or bigBEd in the future) by traversing the proxy # Allow from our internal network # and set the http header to a fake email address, this is required because of galaxy architecture... Satisfy any Order deny,allow Allow from all </LocationMatch> Changes to universe_wsgi.ini host = 0.0.0.0 [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy filter-with = proxy-prefix cookie_path = /galaxy apache_xsendfile = True allow_user_creation = True environment_setup_file = /Volumes/Jose-Drobo/galaxy-dist/.bashrc Cheers Ian

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Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy
by James Taylor 17 Oct '13

17 Oct '13

They are already running a local instance. I didn't realize that bowtie required a different index for colorspace alignment. So Lei, you will have to build the index using bowtie-build -C. -- James Taylor, Associate Professor, Biology/CS, Emory University On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Lei, > > If genomes are not listed, that means that they are not indexed for use with > the tool. The test server is primarily for demonstration or test use > besides, and there could be other unexpected issues even if genomes are > listed (we really do test here). Also, the quotas are very small (10G). If > you want to use this tool, a local, cloud, or slipstream Galaxy is > recommended. Full choices with details are listed here: > http://wiki.galaxyproject.org/BigPicture/Choices > http://usegalaxy.org/toolshed > > Help for setup is here, with the galaxy-dev(a)bx.psu.edu mailing list > available for further support. Tools will need to be installed, and indexes > created. You can rsync the genome, but most genomes will not have loc file > entries and indexes for SOLiD already created - see the Tophat manual for > the command to create these: > http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uni… > http://wiki.galaxyproject.org/Admin/Data%20Integration > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Hopefully this helps! > > Jen > Galaxy team > > > On 10/16/13 11:57 AM, Lei Yan wrote: >> >> Hi all, >> >> We are trying to use “Tophat for SOLiD”. >> But this tool (Tophat for SOLiD) does not seem to be linked to the >> reference genomes that are installed. I can see those genomes on the Tophat >> for illumina tool and the other tools that require a reference genome. >> Please see attachments. >> Does anybody have any ideas for this? Thanks a lot. >> >> >> Lei Yan >> Center for Integrative and Translational Genomics >> The University of Tennessee Health Science Center > > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org >

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galaxy-dev October 2013