- galaxy-dev - lists.galaxyproject.org

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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Galaxy Community Conference Registration Closes May 17
by Dave Clements 10 May '11

10 May '11

Hello all, We are closing registrations for the Galaxy Community Conference at the end of May 17. However, the conference is likely to fill up before that date. So, if you are thinking about attending, *now* is the time to register for the meeting: http://galaxy.psu.edu/gcc2011/Register.html We have also secured some additional rooms on the night of May 24, in a hotel in Lunteren: http://galaxy.psu.edu/gcc2011/Logistics.html Again, it is not necessary to stay in Lunteren the night of May 24, as it is easy to get there from Amsterdam on May 25, before the meeting starts. Finally, a draft schedule is now available at: http://galaxy.psu.edu/gcc2011/Programme.html This is still subject to change, but we are hoping it won't change much. Just 15 days to go! Dave C. -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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problems previewing certain files, downloading files and with login
by Matthew Conte 09 May '11

09 May '11

Good afternoon, I'm having several problems with my local galaxy install which may or may not be related to one another. The first problem I'm having is with the "Display data in browser" feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the "Display data in browser" eyeball icon. It is simply a blank middle panel. The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download: *This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the connection.* In this case, I don't see anything in the log files either. Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page. For this problem, I do get an error in the galaxy log: *Exception happened during processing of request from---------------------------------------- * *('myip', 50593)Exception happened during processing of request from * *('myip', 50594)* *Traceback (most recent call last):* *Traceback (most recent call last):* * File "/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread* * File "/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread* * self.finish_request(request, client_address)* * self.finish_request(request, client_address)* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in finish_request* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in finish_request* * self.RequestHandlerClass(request, client_address, self)* * self.RequestHandlerClass(request, client_address, self)* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in __init__* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in __init__* * self.finish()* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in finish* * self.finish()* * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in finish* *error: [Errno 32] Broken pipe* *----------------------------------------* * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe* I am able to log in via other routes, such as going to "Options->Saved Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScali… Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte(a)umd.edu

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quick question: how can i supply the user's email address to a tool?
by Edward Kirton 09 May '11

09 May '11

is there a variable i can use in the tool config xml file? thanks! ed

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Can I run workflow on certain nodes of the cluster?
by Liisa Koski 09 May '11

09 May '11

Is it possible to run a specific workflow only on certain nodes of the cluster? Either using the API or by setting something in the config files? Thanks, Liisa

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Display BAM with IGV
by Alexander Graf 09 May '11

09 May '11

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 ___________________________________________________________

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Dynamically Specifying PBS Resources
by Allen, Benjamin S 09 May '11

09 May '11

I'm wondering if its possible to somehow present the user with a param that lets him or her specify number of cores, nodes, memory, and wall time from within the workflow for a specific tool. Other than coming up with a predictive algorithm for each tool's resource needs (memory especially) how is one supposed to efficiently use Galaxy and PBS other than somehow letting the user specify needed resources? Think in cases like assembly, for example with Velvet depending on the input files, resource requirements can be vastly different job to job. Thanks, Ben

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shared TEMP directory location
by Shantanu Pavgi 09 May '11

09 May '11

I am configuring galaxy to use a shared filesystem location as it's TEMP directory. I have modified $TEMP variable with the necessary path. Are there any other changes that I need to make? The cluster config page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions about removing or commenting out tool runner configuration, example below: {{{ [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// }}} Should we replace it with some other value or completely remove it? Also, what should it be set to for any additional tools that we install? -- Thanks, Shantanu.

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