Re: [galaxy-dev] Upload files from filesystem paths for non admin users
On 02/03/2011 07:35 PM, Greg Von Kuster wrote: Hello Jean-Baptiste, Running the latest revision in the distribution, (4895:ad933d160a7c), I have followed your steps precisely and do not see the behavior you state. Hello, thank you for having trying to reproduce my problem. I've updated my Galaxy installation, and the problem is gone. Sorry for the delay of my answer, but i just had the time to test it this morning. Regards, Jean-Baptiste ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] local galaxy display problem
Ryan Golhar wrote: I've implemented the Serving Galaxy at a sub directory (such as /galaxy), made the change to Apache, and the universe_wsgi.ini. When I view the page through Apache using http://server.name/galaxy, the page is garbled like something didn't take. Hi Ryan, Did you restart Galaxy after setting up the [filter:proxy-prefix] section and the 'filter-with = proxy-prefix' setting? I did. I restarted both Apache and Galaxy. I verified it using 'ps -ef | grep python' to see that it in fact was shutdown, prior to restarting. Okay, if you're using the static content proxying as in the instructions, can you verify that those paths are correct? For example, the URL: http://server.name/galaxy/static/images/galaxyIcon_noText.png Should display a small icon. --nate ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] local galaxy display problem
Ryan Golhar wrote: SOLVED. I copied/paste the Rewrite rules for apache from the wiki without updating the paths to my installation...once I did that, all worked well. Whoops, I should read ahead before I reply. Glad it's working! --nate On 2/17/11 5:07 PM, Ryan Golhar wrote: I've set up a local instance of Galaxy following the instructions in the wiki for a production instance. I'm running on CentOS with Apache, and a mysql database server. Everything looks great when viewed directly through the Galaxy web server on port 8080. I've implemented the Serving Galaxy at a sub directory (such as /galaxy), made the change to Apache, and the universe_wsgi.ini. When I view the page through Apache using http://server.name/galaxy, the page is garbled like something didn't take. Hi Ryan, Did you restart Galaxy after setting up the [filter:proxy-prefix] section and the 'filter-with = proxy-prefix' setting? I did. I restarted both Apache and Galaxy. I verified it using 'ps -ef | grep python' to see that it in fact was shutdown, prior to restarting. ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Torque drmaa egg
Ryan Golhar wrote: Nevermind (once again). I figured out I need to compile it from the torque... You can also use the 'pbs' job runner, which wraps the PBS C API directly instead of using DRMAA. --nate On 2/17/11 10:30 PM, Ryan Golhar wrote: I'm configuring my local install of galaxy to work with my torque/maui cluster. On the Config/Cluster wiki page, there is mention about telling Galaxy where the DRMAA library is located. The example given points to libdrmaa.so. I've searched my torque installation and haven't come across that library. Does anyone know where this library comes from or where its supposed to be located for torque? ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to login user to local instance
Ryan, congratulations on getting this far! Thank you! :) Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser. First issue - When I go to User - Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org http://usegalaxy.org site. Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this? Try hovering your mouse over the 'User' tab top right of the screen - if you see 'logged in as ' at the top of the popup, then you are logged in. Otherwise not. yeah, I'm definitely not logged in. Something isn't taking. Also, if you have added your login email to the list of admin_users in universe_wsgi.ini (and restarted galaxy of course...), then you can tell you are logged in if you can see an 'Admin' tab - otherwise not. No, I haven't done anything with admin stuff yet. Depending on your situation, you may want to consider using external authentication against (eg) an existing organizational ldap/active_directory or other authentication database and have apache pass the authentication headers through to a proxied galaxy. It's not trivial but the benefit is that users have single sign on - one less password to forget :) I will, but first I want to get the default install working properly before doing anything else. SOI've removed the Apache proxy and am hitting galaxy directly on localhost:8080. Logging in still doesn't work. What else should I check? I'm connected to a mySQL database running on a different server. Could there be a problem there? paster.log doesn't seem to be much help in debugging this... attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to login user to local instance
Ok, I don't know what happened with this...I reinstalled from scratch
and i seems to be working now. I suspect perhaps because I started
galaxy a few times before migrating to mysql. This time, I deleted
everything, changed the config settings then started galaxy.
I'm now on to testing my cluster integration...so, I'm following this:
https://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn
as my initial test. When I run the get flanks, I see the job get
started on the cluster and errors out with the following error:
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py,
line 16, in ?
from galaxy.tools.util.galaxyops import *
File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line
15, in ?
from galaxy import util, jobs, model
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 4, in ?
from galaxy import util, model
File /home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line
11, in ?
import galaxy.datatypes.registry
File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py,
line 6, in ?
import data, tabular, interval, images, sequence, qualityscore,
genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex
File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py, line 7,
in ?
import metadata
File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py,
line 5, in ?
from galaxy.web import form_builder
File /home/galaxy/galaxy-dist/lib/galaxy/web/__init__.py, line 5, in ?
from framework import expose, json, json_pretty, require_login,
require_admin, url_for, error, form, FormBuilder, expose_api
File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 18, in ?
import helpers
File
/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py,
line 29
return (content if len(content) = length else
content[:length].rsplit(' ', 1)[0]+suffix)
^
SyntaxError: invalid syntax
If I submit the job script from the shell, the job runs, but when the
web interface submits the job it doesn't. In both cases, its the galaxy
user account so I don't think environment variables are to blame.
On 2/18/11 10:26 AM, Ryan Golhar wrote:
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have everything set up correctly. I'll test my
cluster integration tomorrow. For now, I can see galaxy from my web
browser.
First issue - When I go to User - Login and try to log myself in
(I've already registered myself), it looks like it works, but the
browser get redirected really fast to another page, then again to
the main page. The User menu never shows me as logged in as it does
on the public usegalaxy.org http://usegalaxy.org site.
Is there a way to check that I'm actually logged in? If its not
showing, then I assume something is wrong. Where do I look to debug
this?
Try hovering your mouse over the 'User' tab top right of the screen - if
you see 'logged in as ' at the top of the popup, then you are
logged in. Otherwise not.
yeah, I'm definitely not logged in. Something isn't taking.
Also, if you have added your login email to the list of admin_users in
universe_wsgi.ini (and restarted galaxy of course...), then you can tell
you are logged in if you can see an 'Admin' tab - otherwise not.
No, I haven't done anything with admin stuff yet.
Depending on your situation, you may want to consider using external
authentication against (eg) an existing organizational
ldap/active_directory or other authentication database and have apache
pass the authentication headers through to a proxied galaxy. It's not
trivial but the benefit is that users have single sign on - one less
password to forget :)
I will, but first I want to get the default install working properly
before doing anything else.
SOI've removed the Apache proxy and am hitting galaxy directly on
localhost:8080. Logging in still doesn't work. What else should I check?
I'm connected to a mySQL database running on a different server. Could
there be a problem there? paster.log doesn't seem to be much help in
debugging this...
___
To manage your subscriptions to this and other Galaxy lists, please use the
interface at:
http://lists.bx.psu.edu/
--
CONFIDENTIALITY NOTICE: This email communication may contain private,
confidential, or legally privileged information intended for the sole
use of the designated and/or duly authorized recipient(s). If you are
not the intended recipient or have received this email in error, please
notify the sender immediately by email and permanently delete all copies
of this email including all attachments without reading them. If you are
the intended recipient, secure the contents in a manner that conforms to
all applicable state and/or federal requirements related to privacy and
[galaxy-dev] cluster path question
I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
It turns out the user's environment is not set up for batch jobs, only the system environment. I too added . ~/.bashrc to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way. On 2/18/11 1:30 PM, Zhibin Lu wrote: Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Ryan Golhar wrote: It turns out the user's environment is not set up for batch jobs, only the system environment. I too added . ~/.bashrc to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way. I'll work on this and release a fix (or instructions for environment configuration) ASAP. On 2/18/11 1:30 PM, Zhibin Lu wrote: Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote: It turns out the user's environment is not set up for batch jobs, only the system environment. I too added . ~/.bashrc to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way. I use TORQUE, but I don't use the drmaa runner. In my case I have no problems with setting the PATH in the .bashrc for the galaxy user on my cluster. Is there a particular reason why you want to use the drmaa runner instead of the PBS runner if your cluster uses TORQUE? On 2/18/11 1:30 PM, Zhibin Lu wrote: Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. golharam.vcfATT1..txt -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
On 2/18/11 2:37 PM, Glen Beane wrote: On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote: It turns out the user's environment is not set up for batch jobs, only the system environment. I too added . ~/.bashrc to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way. I use TORQUE, but I don't use the drmaa runner. In my case I have no problems with setting the PATH in the .bashrc for the galaxy user on my cluster. Is there a particular reason why you want to use the drmaa runner instead of the PBS runner if your cluster uses TORQUE? I couldn't get the pbs_runner to work...so I went with drmaa. On 2/18/11 1:30 PM, Zhibin Lu wrote: Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. golharam.vcfATT1..txt -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without
Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?
All: I retested under IE7 and found the bugs you were mentioning. This has all been fixed on trunk by using a newer local storage library. The only IE7 issue that I am now aware of is when the tool pane is empty when using workflows. Please let me know if you see any other issues. Thanks, K On Mon, Jan 31, 2011 at 1:06 PM, Peter pe...@maubp.freeserve.co.uk wrote: On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, In IE go to Tools - Internet Options - Advanced Tab, then under Browsing section: Uncheck Disable Script debugging (Internet Explorer) Uncheck Disable Script debugging (Other) Check Display a notification about every script error Then you will see the Javascript error when you try to reload the Galaxy page and then try to expand a history item. I would help debug the Galaxy IE issues but I am at work and cannot change these settings on my work computer (the are grey out :( ) -Leandro I had done Disable Script debugging (Internet Explorer) and Display a notification about every script error, but not Disable Script debugging (Other). However I still don't see any javascript error when using Galaxy. Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to login user to local instance
On Fri, Feb 18, 2011 at 5:01 PM, Ryan Golhar golha...@umdnj.edu wrote:
Ok, I don't know what happened with this...I reinstalled from scratch and ...
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py, line
16, in ?
...
File
/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py,
line 29
return (content if len(content) = length else content[:length].rsplit('
', 1)[0]+suffix)
^
SyntaxError: invalid syntax
I deduce you're using Python 2.4, since that line of code
is using the ternary operator added in Python 2.5
http://www.python.org/dev/peps/pep-0308/
Now that it has been reported I think it will be fixed to work with
Python 2.4. However, the Galaxy team have indicated they will
be dropping Python 2.4 (probably this year) so if I were you
since this is a new setup I'd install Python 2.6 on this machine
(Galaxy doesn't yet support Python 2.7).
Peter
___
To manage your subscriptions to this and other Galaxy lists, please use the
interface at:
http://lists.bx.psu.edu/
[galaxy-dev] uploading gzip compressed datasets
Hi all - I'm uploading datasets into my local instance by importing from the filesystem w/o copying into Galaxy. Importing of uncompressed files works properly. The files I'm importing are owned by user1 and a read-able by everyone, including the galaxy user. The galaxy user does not have write permissions in the directory where the files are stored. I have fastq files that are compressed with gzip and owned by user1. I don't want Galaxy to uncompress them, but it appears it is trying to during import, and subsequently fails because of permissions. Is there a way I can force galaxy to import the compressed files w/o uncompressing them? I think most of the mapping programs work on compressed fastq files so I'd rather not uncompressed them to save space. -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
