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

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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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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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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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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Bowtie why it does not take the 1_sequence.txt nor for bowtie nor the Convert
by Olivier Schaad 06 May '11

06 May '11

Dear Sir I try to use Bowtie mapping in galaxy , I import my Illumina s_1_sequence.txt , then I try to use the convert my userName is my email 21: FASTQ Groomer on data 9 An error occurred running this job: /There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have/ but I do have for all the files an error I upload the data using URL http://home.adm.unige.ch/~prnfg/HowardRiezman/wt(RH%20448)%20s_1_sequence.t… http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-1B%20erg3%209f-10A-1B%20s_… http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-9D%20erg3%2013f-9D-9D%20s… http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-13B%20erg3%2013f-9D-13B%2… http://home.adm.unige.ch/~prnfg/HowardRiezman/erg3%20RH%205702%20erg3%20s_1… http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-3A%20erg3%209f-10A-3A%20s_… Could you advice me ? Best regards

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Automatically sending an email to users you've shared a history with
by Leandro Hermida 06 May '11

06 May '11

Hi all, Can Galaxy be configured to automatically send an email to users you have shared a history with (with appropriate link to Galaxy history URL included)? I tried to search the mail list history and could not find, which bring another question, is Google the only way to search the galaxy mailing list archive? regards, Leandro

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Fresh galaxy installation tips/requests
by Assaf Gordon 05 May '11

05 May '11

Hi all, It's been a long while since I had to install a fresh production galaxy server, and I can offer some tips or requests for minor improvements (but to give credit were it's due - installation is much smoother now, and DRMAA works great with SGE out of the box). These are just minor annoyances, but they can help make new installations easier. --- 1. Debugging REMOTE_USER issues. The mix of apache + authentication + non-root URL + load balancing is a killer. googling "mod_rewrite + mod_auth" shows that I'm not the only one having problems with it... Adding those two lines in "./lib/galaxy/web/framework/middleware/remoteuser.py", line 79 is a wonderful debugging tool, which enables you to see what Apache is passing on to Galaxy: for k,v in environ.items(): sys.stderr.write ( "%s:\t%s\n" % ( k, v ) ) I needed to print all environment variables (not just HTTP_REMOTE_USER) so I could debug mod_rewrite's variables setup. If there was an easy way to enable this debug from the INI file it would be a great help. --- 2. The file name "universe_wsgi.ini" is hard-coded in several places. Most of them are python scripts (like cleanup, ampq, etc.), but one is "./galaxy/eggs/init.py". Not a real problem, except that in the "WebApplicationScaling" wiki page it's kind of implied that "universe_wsgi.ini" is not used any more after creating the two separated ini files (universe_wsgi.runner.ini and universe_wsgi.webapp.ini). If you rename "universe_wsgi.ini" instead of copying it, galaxy will simply not start, even if given a different INI file name. So the best recommendation (in the documents) would probably be to maintain three identical INI files, except for the "[server:main]" part of each (and the "enable_job_running = False" in the runner). Most importantly, make sure that the database connection string is identical in all of them. As a side node, the "cp" command in the "WebApplicationScaling" wiki page is incorrect (you can't copy one file into two files). It'll also be good to mention that the cleanup scripts will always use "universe_wsgi.ini" regardless of what the galaxy server is using. --- 3. Saving SGE/PBS/DRMAA shell scripts if "debug=TRUE" in the jobrunner's INI file - this one is a gem, too bad I discovered it too late. If only it was documented :) --- 4. INI keys that accept multiple comma separated values (e.g. "admin_users") are sensitive to white space. Example: admin_users = gordon@cshl.edu,foobar@cshl.edu works fine, but: admin_users = gordon(a)cshl.edu , foobar(a)cshl.edu will not work (spaces around the comma). Same thing with "ucsc_display_sites": ucsc_display_sites = cshl,main will work (and display both "cshl" and "main"), but: ucsc_display_sites = cshl, main will display only "cshl" (because "main" is " main" with a space). It's probably easier to document it than to fix it, but either will do. --- 5. There's no "ensembl_display_sites" in the INI, so disabling the "display at ensembl" link (for BAM files, etc.) requires commenting out the corresponding "<display>" tag in "datatypes_conf.xml", whereas for other servers (gbrowse,ucsc) it's enough to comment out the "ucsc_display_sites" in the INI. --- 6. For galaxy servers running inside an intranet without access to the main/test UCSC Genome browser server, and want to use a local mirror (this might be an obscure setup but that's what I have): disabling both "main" and "test" in "ucsc_display_sites" will disable the authenticated user bypass, because "remouteuser.py" have them hard-coded before setting "self.allow_ucsc_main = True". I needed to patch and add "cshl" as a third option - this is kind of ugly. --- Two development issues not related to production server installation: 1. Debugging complex cheetah templates is very hard. If you have good tricks (beyond #slient and #breakpoint) - examples would be appriciated. If there's a way to see the compiled cheetah code which produced the error - it would be great. One problem is that the error is always reported without a line number (I guess because it's first converted into a string) and without the offending tag. 2. I only half-understand the new "tool_data_table_conf.xml" mechanism - is it explained somewhere ? Looks quite complicated, especially adding in-lined lamba for reading the "__app__" global variable inside the cheetah code of each tool :( --- And user interface quirks: 1. when managing workflows, the "configure your workflow menu" page is a bit uninformative: there's no title, header, instruction or anything else, and the button says "Submit Query" which doesn't mean much ("Update Workflow Menu" would be better). If you click on "configure your workflow menu" and you don't have any workflows, the page is down right mysterious . 2. JQuery Tipsy balloons - please make them go away. Or, make the appearance delay changeable in the INI file (to something like 600 seconds :) ). --- As always, grumbling aside, galaxy is GREAT! so keep up the good work. thanks, -gordon

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Using a Galaxy image on a local system
by Clare Sloggett 05 May '11

05 May '11

Hi all, I would like to set up Galaxy locally. At the moment, I'm just trying to use it on my desktop (a Mac, OSX 10.6.7), but later we will want a local server to play with. Rather than install galaxy and then install all the tools it can use (and deal with OSX issues for some of them), it seems simpler just to use a virtual machine, since there are images which get regularly updated and come with pretty much everything. Is there anything wrong with this approach? I know there are Amazon EC2 images for Galaxy. So far as I know there are not other kinds of images? So for using it on my desktop, I think my options are either to run an EC2-compatible system locally, or to try to convert the AMI to a VMWare or VirtualBox image. I was just wondering if anyone has already tried either of these approaches? Also, is it possible to get hold of the galaxy AMI files themselves? Any advice welcome! Thanks, Clare

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Version Error and Python 2.7
by John David Osborne 03 May '11

03 May '11

I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I'm guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don't believe takes arguments). My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported. -John run_scramble_script(): Executing in /home/galaxy/galaxy_dist/scripts/scramble/build/py2.4/python_daemon: /usr/bin/python -ES scramble.py Traceback (most recent call last): File "scramble.py", line 29, in ? execfile( "setup.py", globals(), locals() ) File "setup.py", line 22, in ? main_module = __import__(main_module_name, fromlist=['version']) TypeError: __import__() takes no keyword arguments scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/nose-0.11.1-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/WebOb-0.8.5-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/PasteScript-1.7.3-py2.4.egg Traceback (most recent call last): File "scripts/scramble.py", line 23, in ? eggs = c.scramble() File "/home/galaxy/galaxy_dist/lib/galaxy/eggs/scramble.py", line 243, in scramble raise last_exc # only 1 failure out of the crate, be more informative galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for python_daemon 1.5.5

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