May 2011 - galaxy-dev - lists.galaxyproject.org

Upload fails, webapp and job runner running on different machines
by Louise-Amélie Schmitt 12 May '11

12 May '11

Hi everyone, I'm currently trying a new galaxy install with the webapp and the job runner running on different machines, sharing a nfs volume where the galaxy files are, and another one where the data is supposed to be stored, as specified in the file_path and new_file_path values in the universe_wsgi files. (one for the webapp and one for the runner, as stated in the doc) Both instances run properly with no error message but when I want to upload a file from wherever in a library, here's what happens: The file's row appears in the library with the "uploading" note. The job is registered in the database. And that's all. Nothing changes afterwards. Nothing is saved anywhere. This can't be a file-too-big issue since the test file I'm working with weighs 3.5kB. I probably stupidly missed something but I really don't see where the problem might be. Any idea? Cheers L-A

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Using wget/curl with Tool Shed?
by Peter Cock 11 May '11

11 May '11

Hi all, I'm trying to download and install something from the Galaxy Tool Shed http://community.g2.bx.psu.edu/ on to our sever. To do this, I'd like to copy/paste the URL of a tool's tar ball (or individual XML file etc) from my browser running on my desktop to a terminal window logged in to our server to give to wget or curl. e.g. This URL will give me bam_to_bigwig_0.0.1.tar.gz if run in a web browser: http://community.g2.bx.psu.edu/common/download_tool?cntrller=tool&id=3b1686… However, the URL actually goes to an HTML page then does some javascript magic to redirect to the real file. I can't easily use this URL with wget or curl. Is this something that you could fix in the website code? For now I can just download the file on my desktop, then scp it to the server (or ssh -X into the server and run a browser from there), but this is an unnecessary hurdle I feel. Regards, Peter

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Community server bug and request
by Assaf Gordon 11 May '11

11 May '11

Tiny bug: When viewing a file inside a tarball, the content-type is forced to "text/plain". Works for most files, but not with image files (example: the "Sequence Logo" tool has a jpg image in the tarball, the browser will display it as text/plain with binary characters). This is done in "./lib/galaxy/webapps/community/controllers/tool.py", function "view_tool_file", line 206: trans.response.set_content_type( 'text/plain' ) regardless of the file type. The complicated solution would be to use the "mimetype" library (http://docs.python.org/library/mimetypes.html) or python-magic (https://github.com/ahupp/python-magic) but a simpler workaround would be to just check the file name for "jpg/png/gif" extensions and change the content-type appropriately. Feature request: A way to easily link to tools, so I can send to them to other people or point them in the right direction. Example: Ross's Web logo tool (great tool, BTW), If I want to tell where it is, the link is: http://community.g2.bx.psu.edu/tool/browse_tools?sort=name&f-state=approved… or direct downloading the tarball is: http://community.g2.bx.psu.edu/common/download_tool?cntrller=tool&id=c2f60f… Both are probably not stable links (if a new version is uploaded). -gordon

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External representation of workflow
by Frederick van Staden 11 May '11

11 May '11

Hello everyone, I need some advice on how to represent the output of all the different tools inside a workflow in an external application. I am looking into using galaxy as a digital evidence processing tool. It is very important that i can access the intermediate sets of data created by every tool's output. Some have suggested the actual tools should populate a database and that the secondary(viewer) application should just retrieve the applicable data form there. Any suggestions? Any input would be greatly appreciated. Regards Fred

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"Hide Datasets" bug in workflow
by Assaf Gordon 11 May '11

11 May '11

Hi, There's a small bug with the "hide dataset" button in the workflow editor - once any dataset is marked as "output" (by clicking on the star icon), there's no way to show all the datasets, even if the user manually un-checked every star icon for every workflow step. meaning: If I have a workflow that *used* to have one step marked as "output", unmarking it (so that no dataset is marked is "output", implying all datasets should be retained in the history) doesn't work - galaxy insists on hiding all the other datasets. Steps to reproduce: 1. Import this workflow: http://main.g2.bx.psu.edu/u/foobar/w/hiddendatasetstest2 2. Edit this workflow. Notice that only the last two steps are marked as "output". don't change anything, close with (or without) saving. 3. Run this workflow. Notice that Steps 1,2,3,5,6 have "Action: Hide this dataset." - as expected. Only steps 4,7 are marked as "output". No need to actually execute the workflow. 4. Edit the workflow again. Remove the "output" mark from steps 4,7 ("Add Column" and "compute"). No dataset is marked as output - at least from the user POV, it's implied that all datasets should be kept in the history (just like when editing a new workflow). Save the workflow, close the workflow. 5. Run this workflow. Notice that steps 1,2,3,5,6 STILL have "Action: hide this dataset" - this is the bug. So the only workaround is to run the workflow, then "extract workflow from history" to get a "clean" copy of the workflow without any datasets hidden. Thanks to Marek Kudla for meticulously experimenting with this issue. -gordon

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Email notification - is workflow is the only way?
by Paul, Rohit (NIH/NCI) [C] 11 May '11

11 May '11

>From what I understand about Galaxy so far, in order to have a user notified that their job has completed, a workflow has to be created in which email notification is chosen as a "Step Action". For the project that I'm currently working on, I need to have a link to one particular workflow appear in the Tools left-hand side panel/frame for every user that logs in to Galaxy. They shouldn't have to import the specific workflow — it should automatically be listed. I know that I can create links in the Tools panel, but it seems that in order to access a workflow (via direct URL such as: '/workflow/run?id=12345') the logged in user has to either be the creator of the workflow or the creator has to have explicitly "shared" the workflow with the user. Is there a way to grant "share" permission on a workflow to all logged-in users, so that I can list it as a Tool link and it shows up for all users, current and those who may register in the future? Or is there some other approach I can/should take to enable job completion notification for all logged-in users? -Rohit

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fasta width formatter
by Owen Hardy 11 May '11

11 May '11

Hi, I set up a local instance on OS 10.6 and was using some fasta tools but noticed fasta width formatter does not execute. Although it shows in my local web interface I do not see width formatter in the tools.conf.xml, nor does the python script appear in /tools/fasta_tools with the others. I also browsed source from central and dist in fasta_tools and do not see it there either...Thanks for any help. An error occurred running this job:/bin/sh: fasta_formatter: command not found zcat: /Users/Owen/Galaxy/galaxy-dist/database/files/000/dataset_190.dat.Z: No such file or directory

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java client
by Reema Popley 11 May '11

11 May '11

Hi i have java client of my tools i need to integrate them in galaxy..so i basically need to convert those java client into xml.....but i m not sure whether java clients can be integrated in galaxy or not...please let me knw d same....Thank you

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Re: [galaxy-dev] Display BAM with IGV
by Nate Coraor 10 May '11

10 May '11

Alexander Graf wrote: > Yesterday I just managed to run Galaxy behind an Apache2 proxy. I followed > the steps described in > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. And > still I encounter the same problem, that the content-length is NULL. I > thought that I could be something with the compression of sending files > (mod_deflate)? > I hope somebody can help me? Hi Alex, I've never used the XSendFile setup myself, perhaps someone with experience with it will comment. Could you ensure that the following is set in your Galaxy config file (universe_wsgi.ini)?: apache_xsendfile = True Also, since you are serving Galaxy from '/galaxy', you may need to change your Location blocks: <Location "/galaxy"> XSendFile on XSendFilePath / # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location> <Location "/galaxy/static"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" </Location> It'd be simpler to serve directly from / if your VirutalHost is dedicated to Galaxy (your DocumentRoot suggests that it is). --nate > > Thanks, > Alex > > My http.conf is: > > <VirtualHost *:80> > DocumentRoot /opt/galaxy > RewriteEngine on > RewriteRule ^/galaxy$ /galaxy/ [R] > RewriteRule ^/galaxy/static/style/(.*) > /opt/galaxy/static/june_2007_style/blue/$1 [L] > RewriteRule ^/galaxy/static/scripts/(.*) > /opt/galaxy/static/scripts/packed/$1 [L] > RewriteRule ^/galaxy/static/(.*) /opt/galaxy/static/$1 [L] > RewriteRule ^/galaxy/favicon.ico /opt/galaxy/static/favicon.ico [L] > RewriteRule ^/galaxy/robots.txt /opt/galaxy/static/robots.txt [L] > RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] > > <Proxy http://localhost:8080> > Order deny,allow > Allow from all > </Proxy> > > <Location "/"> > XSendFile on > XSendFilePath / > # Compress all uncompressed content. > SetOutputFilter DEFLATE > SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary > SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary > </Location> > <Location "/static"> > # Allow browsers to cache everything from /static for 6 hours > ExpiresActive On > ExpiresDefault "access plus 6 hours" > </Location> > </VirtualHost> > > 2011/5/9 Nate Coraor <nate(a)bx.psu.edu> > > > Dave Walton wrote: > > > Could someone who has successfully gotten the IGV tool to work using > > NGINX as your proxy, tell me if there was anything specific they needed to > > do with their NGINX or galaxy config to get it working? > > Hi Dave, > > > > > > It's necessary to set up the more advanced configuration under "Sending > > files using nginx" on the nginxProxy page in the wiki. Could you let us > > know whether you're using that configuration or just a basic > > pass-through proxy? > > > > Thanks, > > --nate > > > > > > > > Thanks, > > > > > > Dave > > > > > > > > > On 4/27/11 9:07 PM, "Dave Walton" <dave.walton(a)jax.org> wrote: > > > > > > I’m getting this same error and I’m running nginx as a proxy server. Is > > there a specfic parameter we should be aware of to allow partial gets? I > > don’t see anything in the wiki page for setting up the ProductionServer. > > > > > > Thanks, > > > > > > Dave > > > > > > > > > On 4/27/11 12:33 PM, "Daniel Blankenberg" <dan(a)bx.psu.edu> wrote: > > > > > > Hi Alex, > > > > > > Displaying BAM files at external applications usually requires an http > > server that supports partial gets. Unfortunately, the current lightweight > > http server that is built into Galaxy does not support these advanced http > > options. However, this limitation can be overcome by using a proxy server > > that is able to handle http1.1 requests. Please see "Using a Proxy server" > > at > > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServerfor help on setting this up. > > > > > > Thanks for using Galaxy, > > > > > > Dan > > > > > > > > > On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote: > > > > > > Hello all, > > > I just updated our local copy of Galaxy and just wanted to try the new > > IGV display application. > > > When I try to display a BAM file with the local IGV or the web IGV I > > encounter following error complaining about the Null content-length. > > > Has any of you encountered the same problem? Do I miss something? > > > Thanks in advance > > > > > > Alex > > > > > > > > > INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] > > Loading1 resources. > > > ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] > > Null content-length for: > > http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… > > > ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error > > loading sam track > > > java.lang.RuntimeException: Error loading file: > > http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… content-length > > > at > > org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) > > > at > > org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) > > > at > > org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) > > > at > > org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) > > > at > > org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) > > > at > > org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) > > > at > > org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) > > > at > > org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) > > > at > > org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) > > > at > > org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) > > > at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) > > > at org.broad.igv.track.TrackManager.load(TrackManager.java:271) > > > at > > org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) > > > at > > org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) > > > at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) > > > at > > org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) > > > at > > org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) > > > at org.broad.igv.main.CommandListener.run(CommandListener.java:93) > > > at java.lang.Thread.run(Thread.java:636) > > > ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] > > java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: > > > > http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… content-length > > > > > > > > > > > > ___________________________________________________________ > > > > > > Alexander Graf > > > > > > Laboratory of Functional Genome Analysis > > > Gene Center, University of Munich (LMU) > > > Feodor-Lynen-Strasse 25; 81377 Munich; Germany > > > email: graf(a)lmb.uni-muenchen.de > > > Internet: www.lafuga.de/genomics.htm < > > http://www.lafuga.de/genomics.htm> > > > ___________________________________________________________ > > > > > > ___________________________________________________________ > > > 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/ > > > > > > > > > > > > > > ___________________________________________________________ > > > 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/ > >

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How disable browser forward and backward buttons from galaxy.
by hari krishna 10 May '11

10 May '11

Hi, In galaxy after logout if i press browser back button, it takes me to my previous login page. For this , in our galaxy instance we modified welcome.html and templates/user/logout.mako and added the following java script: <script language="JavaScript"> javascript:window.history.forward(1); </script> still the browser back button works asusual. please suggest me where all pages i need to modify... -- Thanks & Regards, Hari Krishna .M

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