[galaxy-dev] Emailing to all our Galaxy users
Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/
Re: [galaxy-dev] Emailing to all our Galaxy users
On Mon, Aug 6, 2012 at 9:14 AM, Joachim Jacob joachim.ja...@vib.be wrote: Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim Do you mean the registered accounts on your local Galaxy instance? This lives in the database of course, but is also available via the admin pane, see http://wiki.g2.bx.psu.edu/Admin/Interface or the reports web application (sh run_reports.sh - see also reports_wsgi.ini for the default port etc). Peter ___ 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/
Re: [galaxy-dev] Emailing to all our Galaxy users
Hi Joachim Go to Admin Menu - Security - Manage users. This will give you a list of all users. Alternatively, use the reports tool: Users - Date of last login and select 0 days Hope this helps, Regards, Hans On 08/06/2012 10:14 AM, Joachim Jacob wrote: Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim ___ 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/
Re: [galaxy-dev] Emailing to all our Galaxy users
Dear Peter and Hans-Rudolf, Everyday I learn something new about Galaxy :-) Thanks for pointing out the run_reports.sh service! This feels like what I need. Somehow I had never heard of it... Cheers, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 08/06/2012 10:25 AM, Hans-Rudolf Hotz wrote: Hi Joachim Go to Admin Menu - Security - Manage users. This will give you a list of all users. Alternatively, use the reports tool: Users - Date of last login and select 0 days Hope this helps, Regards, Hans On 08/06/2012 10:19 AM, Peter Cock wrote: On Mon, Aug 6, 2012 at 9:14 AM, Joachim Jacob joachim.ja...@vib.be wrote: Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim Do you mean the registered accounts on your local Galaxy instance? This lives in the database of course, but is also available via the admin pane, see http://wiki.g2.bx.psu.edu/Admin/Interface or the reports web application (sh run_reports.sh - see also reports_wsgi.ini for the default port etc). Peter On 08/06/2012 10:14 AM, Joachim Jacob wrote: Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim ___ 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/
[galaxy-dev] queue question
Hi There, I'm not sure if this is the correct address to email to, so apologies in advance if I am in error. I am using the Galaxy Main (publicly available) site. I am wondering if there is a way to tell where my job is in the queue - in other words, how long it will be until my job begins to run and also ,how long until the run is done. I submitted a Bowtie paired end alignment last night (8.5.12) and the history states that my job is still waiting to run (grey). Thank you, Lillian Zwemer Lillian Zwemer, PhD Mother Infant Research Institute Tufts Medical Center The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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/
[galaxy-dev] Different User with Torque
I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization. ___ 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/
Re: [galaxy-dev] Different User with Torque
On Aug 6, 2012, at 1:01 PM, Wood, James, D james.wo...@topper.wku.edu wrote: I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization. Hi James, I am in the same situation as you are. The basic documentation is at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User. However, there could be some site-specific issues with that configuration. For instance the user names in my instance do not correspond to the uid part of the galaxy username (email address), which is what released galaxy-dist code assumes. Fortunately, Nate and Scott from the Core Galaxy Team helped me get through almost all of the issues while we were at the Galaxy Community Conference. I am still working through the single remaining issue of drmaa not passing modified resource requests to Torque, but the rest appears to work stably with Torque 2.5.12. Regards, Alex___ 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/
[galaxy-dev] Galaxy output not showing on tool success, indicating job failure.
Hello. I am an undergraduate working on a tool very similar to Tophat.
My question is probably very basic, but I am having issues displaying
the output. I am assuming is giving me the failed run boxes, even though
my tool completes execution and generates its files.
Note that I am not working on a cluster, as I am simply trying out
galaxy with this tool.
I have modified universe_wsgi.ini cleanup_job = onsuccess to keep the
output from being deleted due to the failure. Every file that is queued
up in the history pane for each run appears in the working directory
after execution, and I confirm successful runs with stdout and logs. If
you click on the boxes in the history pane, you can download the output
files correctly. I just cannot see previews of them or see them in the
middle screen.
output in my tool XML is specified as follows:
data format=sam name=alignments label=${tool.name} on
${on_string}: alignments from_work_dir=mapsplice_out/alignments.sam /
where mapsplice out is a sub directory created to contain all output of
my command line tool. The reason I have it contained is because it runs
its own combine and clean-up jobs before it is done executing, and you
are left with logs. If you do not specify 'from_work_dir' in the output,
the output files are there, but if you do specify, galaxy seems to be
moving them into the database.
stderr prints: (also I am aware stderr causes galaxy failures, I have
nothing printing to stderr)
/home//galaxy-dist/database/files/000/dataset_387.dat is fasta format
which suggests to me that galaxy is trying to copy the contents of the
output files into this particular file which is not what needs to
happen. If I do not include the optional from_work_dir in the data
tag I am not able to download the files that are created.
On the wiki, the output tag set says that You specify the number and
type of your output files using the containeddatatags. You must pass
them to your tool executable through using line variables just like the
parameters described in the previous sections.
For this, I have created variables to hold the output and pass them
in the command string, but my tool takes no parameters to specify
output. It simply creates various output files based on the parameters
passed in. However it still runs regardless.
The preview I get after execution is the print to stdout (exact copy of
the log) that indicate a successful run.
I apologize for the length, I am just trying to give most the helpful
information. If more is needed, let me know. I am running my own
instance of galaxy.
John P - Undergraduate Research
University of Kentucky Bioniformatics
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[galaxy-dev] How to configure samtools in galaxy on cluster
Recently, I am trying to configure our galaxy on our cluster with PBS submission. I run galaxy locally very well on the head node, but I met one issue when I tried to configure galaxy on our cluster. In universe_wsgi.ini file, I added the following entries, start_job_runners = pbs default_cluster_job_runner = pbs:/// And then I run the command to generate an egg, LIBTORQUE_DIR=/usr/lib64/libtorque python scripts/scramble.py -e pbs_python --config=universe_wsgi.ini Then I run galaxy and submitted two jobs into the PBS queue. I checked the galaxy log and PBS queue and found these two jobs were submitted successfully. But after a while, galaxy told me that the two jobs were failed. I suspected I did not modify the galaxy:tool_runners section in the universe_wsgi.ini file. The node machines cannot find the 3rd party tools. Can anyone give me some advices? Thanks a lot! ___ 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/
Re: [galaxy-dev] Different User with Torque
It looks like the Torque provided libdrmaa.so does not support DRMAA native options. I built a 3rd party library (http://apps.man.poznan.pl/trac/pbs-drmaa/wiki) and was able to successfully run text galaxy jobs under a real user id with a correct resource request specified through the dynamic runner as a native DRMAA option. The only remaining step is to populate the galaxy_user.username from our LDAP. All modified galaxy code has been provided to the core Galaxy Team by the way. Cheers, Alex On Aug 6, 2012, at 1:16 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: On Aug 6, 2012, at 1:01 PM, Wood, James, D james.wo...@topper.wku.edu wrote: I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization. Hi James, I am in the same situation as you are. The basic documentation is at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User. However, there could be some site-specific issues with that configuration. For instance the user names in my instance do not correspond to the uid part of the galaxy username (email address), which is what released galaxy-dist code assumes. Fortunately, Nate and Scott from the Core Galaxy Team helped me get through almost all of the issues while we were at the Galaxy Community Conference. I am still working through the single remaining issue of drmaa not passing modified resource requests to Torque, but the rest appears to work stably with Torque 2.5.12. Regards, Alex ___ 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/
[galaxy-dev] Error on database_connection statement in universe_wsgi.ini file
Hello, Galaxy runs fine 'out of the box' with the default universe_wsgi.ini initialization file. But when I change the database_connection statement to connect to my MySql database, I get the errors below. Can you please tell what the problem is? Thanks! -Wolf. Modification to universe_wsgi.ini file: #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock - Then when I type sh run.sh I get this: - wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 313, in loadapp **kw) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 413, in get_context section) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py, line 1997, in parse src ValueError: (EntryPoint must be in 'name=module:attrs [extras]' format, 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock') ___ 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/
