- galaxy-dev - lists.galaxyproject.org

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.

2 1

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.

2 1

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.

1 1

problem integrating new jar file
by vijayalakshmi 17 Jun '13

17 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.

4 3

transferring Trapnell et al programs into a one user instance of Galaxy
by Elwood Linney 17 Jun '13

17 Jun '13

Hello again, I guess I now realize why there is so much traffic on the user list about tools, and I also can guess that while the online directions for dealing with them are written well for those individuals familiar with administration a server or doing full time bioinformatics, but there are some of us computer numbskulls that need something like a Galaxy transfer booklet for computer idiots (biologists) to transfer what we want into a single user or single lab setup. I am hoping there is someone out there like myself who worked through the problem of transferring the Trapnell et al series of programs into a Mac Pro desktop, namely NGS: RNA Analysis 1) Tophat for Illumina tophat (1.3.3-1.4.0) with bowtie + bowtie indexes 2) Cufflinks cufflinks (1.3.0-2.1.1) 3) Cuffcompare cufflinks (1.3.0-2.1.1) 4) Cuffmerge cuffmerge (1.3.0-2.1.1) 5) Cuffdiff cuffdiff (2.1.0-2.1.1) I have transferred the galaxy framework in a work/galaxy-dist pathway unto a solid state drive of a 64gb ram mac that has 3 other 2tb drives and have gotten some valuable advice for transferring large datasets from the same computer via admin. For the next year at least my needs with be just the RNA analysis tools above. Any help will be greatly appreciated. My intention here is remove my contribution to the traffic on the online Galaxy, so some people should consider it a worthy cause Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Cener

2 1

wiki surge protection broken
by Brian Craft 15 Jun '13

15 Jun '13

Followed a google result to the wiki, and got a "surge protection" warning: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Unless you're protecting from "surges" of 0.5 - 1 pages per hour, your surge protection is broken.

1 0

docs for data_source.py, file type handling, etc.
by Brian Craft 15 Jun '13

15 Jun '13

I'm trying to add a data source that provides tarballs. Are there any docs for data_source.py, the data types registry, and so-forth? The data source docs seem to only cover the http callback mechanism. I'm trying to understand what happens after that: a json file is created with download params, data_source.py reads it and then overwrites it with the downloaded file, the registry is consulted for additional processing, which then gunzips the tarball. Gunzip isn't necessarily the right step. It might be better to tar-extract appropriate files and let galaxy know about them somehow. I can call data_source.py from a custom tool, and then handle the tar steps, but I don't know how to direct galaxy to the untarred files.

1 0

nglims/services/python
by Lee Katz 15 Jun '13

15 Jun '13

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

2 1

printing output from java tool in the middle pane in galaxy
by vijayalakshmi 14 Jun '13

14 Jun '13

Hi all, I am trying to integrate a tool written in java into galaxy. The java code will output a GUI window. I want to know how to output that window in the middle pane Thanks, VJ

1 0

How to speed up submissions of workflows
by Thon Deboer 14 Jun '13

14 Jun '13

Hi, I am routinely running hundreds of pair-end sequencing runs and find that STARTING a workflow on all of these can easily take hours since it seems each workflow preparation takes about 3 minutes, so for doing 128 fastq pairs like this it will take over 3 hours just to get all workflows running.. Is there any way for me to speed up this process, maybe by adding more handlers (although I am suspecting the WEB server is the bottleneck here)? I already run 8 handlers but only one web server. I could loadbalance the webservers through my proxy server.Will that speed up the submissions or are we stuck with this linear process? Thanks, Thon

2 1