Re: [galaxy-dev] Galaxy reports
Hi Philippe, I realised we hadn’t restarted the reports application after the upgrade. I’ve done that it seems to be working fine. Cheers. Steve McMahon Solution Architect and Senior System Administrator | Scientific Computing Information Management and Technology CSIRO T +61 2 6214 2968 Alt +61 4 0077 9318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.au 1 Wilf Crane Crescent, Yarralumla ACT 2600 PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Martin Cech Sent: Friday, 7 March 2014 9:09 AM To: Philippe Moncuquet Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy reports Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.commailto:philippe.m...@gmail.com wrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy + google analytics?
Thanks Ron,
This will be a big help.
Cheers.
Steve McMahon
Manager, ASC Cluster Services
Information Management Technology (IMT)
CSIRO
Phone: +61-2-62142968 | Mobile: +61-4-00779318
steve.mcma...@csiro.au | www.csiro.au
PO Box 225, DICKSON ACT 2602
1 Wilf Crane Crescent, Yarralumla ACT 2600
-Original Message-
From: Ron Horst [mailto:r.ho...@uq.edu.au]
Sent: Wednesday, 3 July 2013 12:09 AM
To: McMahon, Steve (CSIRO IMT, Yarralumla); galaxy-dev@lists.bx.psu.edu
Subject: RE: Galaxy + google analytics?
Steve
The GVL project has done it
In template/base.mako template/base/*.mako, add the following, where UA-
= your Google Analytic user account
script type=text/javascript
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-nn']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript';
ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' :
'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
})();
/script
Ron
Genomics Virtual Lab
Uni Qld
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of steve.mcma...@csiro.au [steve.mcma...@csiro.au]
Sent: Tuesday, 2 July 2013 12:10 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Galaxy + google analytics?
Has anyone hooked Galaxy up to Google analytics? We get great reporting from
the Galaxy reports interface but we don't get number of connections and some
other things that Google analytics would give us.
:)
Sent from my iPad
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[galaxy-dev] Galaxy + google analytics?
Has anyone hooked Galaxy up to Google analytics? We get great reporting from the Galaxy reports interface but we don't get number of connections and some other things that Google analytics would give us. :) Sent from my iPad ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] PBS_Python Unable to submit jobs
Hi Carrie, I've had the same problem. I wanted to get Galaxy to submit to a cluster which was running Torque 4.x. Torque clients need to be 4.x to work with the that version of the server. I spent a bit of time looking into this and determined that pbs_python used by Galaxy is not compatible with Torque 4.x. A new version would need to be built. At that stage I investigated using the DRMAA runner to talk to the Torque 4.x server. That did work if I built the Torque clients with the server name hard coded --with-default-server. What the DRMAA runner didn't do was data staging as the PBS runner does. So I started working on some code for that. I'm looking at giving up on the data staging by moving the Galaxy instance to the cluster. Sorry I didn't help. I would be interested in comments from Galaxy developers about whether the PBS runner will be supported in the future and, hence, whether Torque 4.x will be supported. I'm also interested whether the DRMAA runner will support data staging or whether Galaxy instances really need to share file systems with a cluster. Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ganote, Carrie L Sent: Friday, 5 April 2013 4:52 AM To: galaxy-...@bx.psu.edu Subject: [galaxy-dev] PBS_Python Unable to submit jobs Hi Galaxy dev, My setup is a bit non-standard, but I'm getting the following error: galaxy.jobs.runners.pbs WARNING 2013-04-04 13:24:00,590 (75) pbs_submit failed (try 1/5), PBS error 15044: Resources temporarily unavailable Here is my setup: Torque3 is installed in /usr/local/bin and I can use it to connect with (Default) server1. Torque4 is installed in /N/soft/ and I can use it to connect to server2. I'm running trq_authd so torque4 should work. I can submit jobs to both servers from the command line. For server2, I specify the path to qsub and the servername (-q batch@server2). In Galaxy, I used torquelib_dir=/N/soft to scramble pbs_python. My path is pointing at /N/soft first so 'which qsub' returns torque4. If I just use pbs:///, it will submit a job to server1 (shouldn't work, because /N/soft/qsub doesn't work from the commandline, since the default server1 is running torque3). If I use pbs://-l vmem=100mb,walltime=00:30:00/, it won't work (the server string in pbs.py becomes -l vmem=100mb,walltime=00:30:00 intsead of server1) If I use pbs://server2/, I get the Resources temp unavail error above. The server string is server2, and I put the following in pbs.py: whichq = os.popen(which qsub).read() stats = os.popen(qstat @server2).read() These return the correct values for server2 using the correct torque version4. I'm stumped as to why this is not making the connection. It's probably something about the python implementation I'm overlooking. Thanks for any advice, Carrie Ganote ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] pbs_python and torque 4.x
Hi all, We are trying to get our instance of Galaxy submitting jobs to a cluster a using the staged method referred to at http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Our cluster is running Torque 4.1.3. We need to use Torque 4.x clients to be able to submit jobs to it. I've set up our Galaxy server to be able to submit jobs and stage data in and out. Galaxy can't submit jobs to the cluster, however. The problem seems to be with pbs_python. On the associated wiki there is a ticket for the problem and I have been able to reproduce it. https://oss.trac.sara.nl/pbs_python/ticket/31 Has anyone had any experience with getting pbs_python to work with Torque 4.x? Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 ___ 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] running functional tests on a galaxy server
Hi Chris and Nate, I'm also interested in being able to run functional tests against either our production server or a test server with an identical setup to make sure that not only the tools are working but their interaction with various compute resources are also working etc. If we get this going we would like to run this automatically and regularly so that administrators and users will be able to see whether particular tools are working or not. Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 ___ 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] tool shed offline?
Hi, This is my first post to this list. I'm working on a Galaxy service within CSIRO in Australia. I can't seem to access http://toolshed.g2.bx.psu.edu/ at the moment. Is it offline or is there something else between here and there preventing the access? Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 ___ 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] tool shed offline?
Thanks Ross for the trick :) Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 From: Ross [mailto:ross.laza...@gmail.com] Sent: Wednesday, 1 February 2012 4:50 PM To: McMahon, Steve (CSIRO IMT, Yarralumla) Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] tool shed offline? Hi, Steve. Looks like it's down. They'll all wake up over there in about 8 hours or so For future reference this is a useful trick: http://www.downforeveryoneorjustme.com/http://toolshed.g2.bx.psu.edu/http://www.downforeveryoneorjustme.com/http:/toolshed.g2.bx.psu.edu/ On Wed, Feb 1, 2012 at 4:44 PM, steve.mcma...@csiro.au wrote: Hi, This is my first post to this list. I'm working on a Galaxy service within CSIRO in Australia. I can't seem to access http://toolshed.g2.bx.psu.edu/ at the moment. Is it offline or is there something else between here and there preventing the access? Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968tel:%2B61-2-62142968 | Mobile: +61-4-00779318tel:%2B61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
