June 2013 - galaxy-dev - lists.galaxyproject.org

trimest tool cuts the begining of my seq names in the output fasta file
by Inbar Plaschke 18 Jun '13

18 Jun '13

Dear galaxy developers, When I use the EMBOSS tool: trimest<https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos…>, Trim poly-A tails off EST sequences , within galaxy The sequences names in the fasta output file comes out without their beginning, for instance: >gi|259479195|dbj|AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds Will be shortened into: >AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds How can I keep the beginning of the sequence names? Am I doing something wrong? Many thanks for your help Inbar [Description: logo_50prcnt] Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Building 51, room 323 Email: inbarpl(a)bgu.ac.il<mailto:inbarpl@bgu.ac.il> Tel: +972-8-6428676 Fax: +972-8-6479035 Web: http://bioinfo.bgu.ac.il<http://bioinfo.bgu.ac.il/>

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Best practices for a local install of Galaxy for only 1 user on a Mac
by Paul St. Amand 18 Jun '13

18 Jun '13

I am trying to install Galaxy on a new iMac (i7, 32gb ram, OSX 10.8). Mostly the install worked and I can use my local install. However, about 25% of the functional tests failed for me. And about 4 of the unit tests failed for me. Also, I can't seem to install anything from the toolshed (logged in as Admin). Below is what I did to install. Can any Galaxy/Mac gurus out there please fix the errors in the below install list so that we can have a good idea of the best practices for installing Galaxy on a Mac running the latest version of OSX? Also, tips for installing all of the dependencies would be great too. Best practices for a local install of Galaxy for only 1 user on a Mac. For Galaxy on a Mac (OSX 10.8): To uninstall: delete galaxy-dist folder (should anything else be done??) To install Galaxy on a Mac (OSX 10.8): 1. Install Mercurial, download latest version from http://mercurial.selenic.com/mac/ and unzip and run installer. 2. Run the following in the terminal as a NON-root user (change "pst" to your user ID). (Is it better to create a "galaxy" user and install as user "galaxy"???) (Is it OK to use /Users/MacID/Applications as the install location, or is the home folder best??): % cd /Users/pst/Applications % hg clone https://bitbucket.org/galaxy/galaxy-dist/ % cd /Users/pst/Applications/galaxy-dist % hg update stable 3. After install, run this to start the server and create defaults, then Control-C to quit the server: % cd /Users/pst/Applications/galaxy-dist % sh run.sh % Ctrl-c in the terminal 4. Make the following changes to the universe_wsgi.ini file (found in /Users/pst/Applications/galaxy-dist/) using any text editor, save file as a UNIX text only file (TextWrangler works great for this) (What other changes should be made?). library_import_dir = /Users/pst/Documents/GalaxyDataFiles allow_library_path_paste = True admin_users = yourID(a)yourLocation.com allow_user_dataset_purge = True debug = False use_interactive = False cleanup_job = onsuccess 5. Set Up Visualizations: % cd /Users/pst/Applications/galaxy-dist % cp datatypes_conf.xml.sample datatypes_conf.xml 6. Get wigToBigWig and bedGraphToBigWig from (http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/) and copy the files to the /Users/pst/Applications/galaxy-dist/ folder. 7. Set both files to be executable: % chmod +x /Users/pst/Applications/galaxy-dist/bedGraphToBigWig % chmod +x /Users/pst/Applications/galaxy-dist/wigToBigWig 8. Test installation with: % cd /Users/pst/Applications/galaxy-dist % sh run_functional_tests.sh 9. Check test output. The above command will output an html file called "run_functional_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests. 10. Other tests: % cd /Users/pst/Applications/galaxy-dist % sh run_unit_tests.sh 11. Check test output. The above command outputs an html file called "run_unit_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests. 12. Install dependencies?? To start the local Galaxy server: % cd /Users/pst/Applications/galaxy-dist % sh run.sh To use the local Galaxy server, enter this URL in your web browser: http://localhost:8080 To stop the Galaxy server, just hit Ctrl-c in the terminal window from which Galaxy is running. To see if new releases are available: % cd /Users/pst/Applications/galaxy-dist % hg incoming If "no changes found" then you are up to date. If changes are found, then add new versions with: % hg pull -u To update local galaxy: % cd /Users/pst/Applications/galaxy-dist % hg update stable

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dynamically load and run R scripts
by Keilwagen, Jens 17 Jun '13

17 Jun '13

Hi guys, I was searching for a possiblity to dynamically load and run R scripts and I found http://dev.list.galaxyproject.org/dynamic-loading-of-tools-tt4138600.html I know that it might be a security issue, but we only have a local instance here. Optimally an R script can be loaded into the history. Subsequently, this script can be execute via "tool" that takes this script and some parameters and returns the result. Is anything like that out there? Could anyone give me a reference? Thanks a lot, Jens

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The requested URL /cgi-bin-root/hgTracks was not found on this server
by Rodolfo Aramayo 17 Jun '13

17 Jun '13

Hi, I starting getting this error since late galaxy update I get data from UCSC Main (local), but when I click "display at UCSC main" I get: Not Found The requested URL /cgi-bin-root/hgTracks was not found on this server. Please help Thanks --R

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invalid frame access with data source
by Brian Craft 17 Jun '13

17 Jun '13

When loading a data source in an iframe, the galaxy js is doing some sort of invalid probing of the frame, leading to this error: Blocked a frame with origin "http://pk:8080" from accessing a frame with origin "https://tcga1.kilokluster.ucsc.edu". pk:8080 is the galaxy frame. Here is the offending code: jQuery( function() { $("iframe#galaxy_main").load( function() { $(this).contents().find("form").each( function() { What is this? And is there some way to work around it? On chrome it doesn't appear to cause any problem, however on FF it causes the js to abort in both frames, preventing the data source callback. b.c.

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Cloudman - can you specify the volume size without needing to access the instance URL?
by Ravpreet Setia 17 Jun '13

17 Jun '13

It is quite tedious to do so if you have many instances running. Is there a way to automate this step? Thanks.

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bowtie2 on galaxy cloudman?
by Murphy, Theresa 17 Jun '13

17 Jun '13

Is bowtie2 available on galaxy cloudman? If not, when will it be available? Thanks, Theresa Murphy The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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Cloudman - Can you label volumes after user specifies the volume size they want?
by Ravpreet Setia 17 Jun '13

17 Jun '13

Initially only one volume is shown on Amazon's EC2 management console. Then, after the user goes into the instance's URL and logs into Cloudman, they are prompted with a box called "Initial cluster configuration" where they specify the size of the volume they want. THEN, three nameless volumes are produced. The problem here is that the volumes are nameless, and this makes cleanup on Amazon's EC2 console difficult since we have no way of knowing these volumes are related to the Galaxy cloudman AMI. I am wondering if there is a way to pass a script to Cloudman that it will run once the volumes are created (ie. After the user goes to the URL and specifies the volume size they want). The script will be used to add name= tags for each of the three additional volumes. Thanks.

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Re: [galaxy-dev] nglims/services/python
by Lee Katz 17 Jun '13

17 Jun '13

Thanks Ross! Unfortunately I still have the same error. Although I can directly run galaxy via the command run.sh, the system service fails with the error I showed before. In other words this works as the galaxy user: ./run.sh --restart This does not work when I run it as root (or when root runs it as the machine starts up): service chapman-galaxy start This is the init file which I slightly modified from the contrib directory (which now resides under /etc/init.d/). There must be some fundamental reason why running it as root does not work that I don't understand. I actually don't think it's this init script that is the problem because a vanilla install of Galaxy works fine using "system galaxy start" and when it is under init.d. #!/bin/bash # Author: James Casbon, 2009 # Modified by Lee Katz 2013 for this specific system ### BEGIN INIT INFO # Provides: chapman-galaxy # Required-Start: $network $local_fs $mysql # Required-Stop: # Default-Start: 2 3 4 5 # Default-Stop: 0 1 6 # Short-Description: Chapman-Galaxy ### END INIT INFO . /lib/lsb/init-functions USER="galaxy" GROUP="galaxy" DIR="/home/galaxy/bin/chapman-dist" PYTHON="/usr/bin/python" OPTS="-ES ./scripts/paster.py serve --log-file $DIR/galaxy.log universe_wsgi.ini" PIDFILE="/var/run/galaxy-chapman.pid" case "${1:-''}" in 'start') log_daemon_msg "Starting Chapman-Galaxy" if start-stop-daemon --chuid $USER --group $GROUP --start --make-pidfile \ --pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON -- $OPTS; then log_end_msg 0 else log_end_msg 1 fi ;; 'stop') log_daemon_msg "Stopping Chapman-Galaxy" if start-stop-daemon --stop --pidfile $PIDFILE; then log_end_msg 0 else log_end_msg 1 fi ;; 'restart') # restart commands here $0 stop $0 start ;; 'status') if [ -f "$PIDFILE" ]; then pid=`cat $PIDFILE`; log_daemon_msg "Chapman-galaxy pid is $pid" else log_daemon_msg "Chapman-galaxy does not have a pid" fi ;; *) # no parameter specified echo "Usage: $SELF start|stop|restart|reload|force-reload|status" exit 1 ;; esac On Sat, Jun 15, 2013 at 12:38 AM, Ross <ross.lazarus(a)gmail.com> wrote: > My mistake - try > (sudo) pip install pyaml > That's what the pip yaml repo is called... > > > > On Sat, Jun 15, 2013 at 11:38 AM, Ross <ross.lazarus(a)gmail.com> wrote: > >> Hi, Lee - the last line of that error dump might be worth thinking about. >> It seems clear enough. Your python interpreter seems unable to import a >> module called yaml >> >> Perhaps you need to (eg) do >> pip install yaml >> in the virtualenv (or sudo ... for the system one if not using a >> virtualenv) you're running your Galaxies with? >> I hope this helps. >> >> >> On Fri, Jun 14, 2013 at 11:52 PM, Lee Katz <lskatz(a)gmail.com> wrote: >> >>> Hi, I am running into an error that I bet has a simple solution. I would >>> appreciate any help. Thanks. >>> >>> I am running Brad Chapman's LIMS extension locally on Ubuntu 12. I also >>> installed it as a service under /etc/init.d/chapman-galaxy using >>> contrib/galaxy.debian-init . It works when I run it directly (./run.sh >>> --reload) >>> >>> When I run a version of Galaxy without nglims as a service, there is no >>> error. >>> When I run a version of Galaxy with nglims, not as a service (run.sh), >>> there is no error. >>> However, when I run the same version of Galaxy with nglims as a service, >>> there is an error. I don't understand well enough what the difference is >>> when I run it as a service to diagnose this problem. The lines leading to >>> the error from the log file is below. Something to do with yaml not being >>> loaded, but I know I installed python-yaml through aptitude. >>> >>> galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,873 Enabling >>> 'requests' controller, class: Requests >>> galaxy.webapps.galaxy.controllers library_common >>> galaxy.webapps.galaxy.controllers.library_common >>> galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,874 Enabling >>> 'library_common' controller, class: LibraryCommon >>> galaxy.webapps.galaxy.controllers nglims >>> galaxy.webapps.galaxy.controllers.nglims >>> Traceback (most recent call last): >>> File "./scripts/paster.py", line 34, in <module> >>> command.run() >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", >>> line 84, in run >>> invoke(command, command_name, options, args[1:]) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", >>> line 123, in invoke >>> exit_code = runner.run(args) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", >>> line 218, in run >>> result = self.command() >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", >>> line 276, in command >>> relative_to=base, global_conf=vars) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", >>> line 313, in loadapp >>> **kw) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", >>> line 204, in loadapp >>> return loadobj(APP, uri, name=name, **kw) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", >>> line 225, in loadobj >>> return context.create() >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", >>> line 625, in create >>> return self.object_type.invoke(self) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", >>> line 188, in invoke >>> filtered = context.next_context.create() >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", >>> line 625, in create >>> return self.object_type.invoke(self) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", >>> line 110, in invoke >>> return fix_call(context.object, context.global_conf, >>> **context.local_conf) >>> File >>> "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py", >>> line 57, in fix_call >>> val = callable(*args, **kw) >>> File >>> "/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/buildapp.py", line >>> 44, in app_factory >>> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) >>> File >>> "/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/__init__.py", line >>> 274, in add_ui_controllers >>> module = import_module( module_name ) >>> File >>> "/home/galaxy/bin/chapman-dist/lib/galaxy/util/backports/importlib/__init__.py", >>> line 37, in import_module >>> __import__(name) >>> File >>> "/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py", >>> line 24, in <module> >>> import yaml >>> ImportError: No module named yaml >>> >>> >>> >>> -- Lee Katz, Ph.D.

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problem integrating new jar file
by vijayalakshmi 16 Jun '13

16 Jun '13

Hi, I am trying to integrate a tool that is written in java into galaxy. The following is what I've done. 1) Created a directory inside /tools directory and put my xml and runnable jar file in it. 2) Linked the xml file in 'tool_conf.xml'. *tool_conf.xml* <section name="sample tool" id="sample_tool"> <tool file="Sample/sample.xml"/> </section> *sample.xml* <tool id="sample" name="Compute correlation"> <command>java -jar sample.jar</command> </tool> *sample.java* (exported into a runnable jar file from eclipse) package Sample; public class Sample { public static void main(String[] args) { System.out.println("Hello world this is important"); } } When I run the above, (i.e when I click on execute in the middle pane), nothing gets added to my current history. Since there is no visual output of any sort, I am not able to figure out where the problem lies. Any help or pointer is appreciated! Thanks y'all! VJ.

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