Re: [galaxy-dev] Knowing who is currently logged into your system

Ok. Yes the rebooting is a pity. However there are opportunities to use tools without restart by using toolsheds. We are currently investigating that in more detail. It doesn't work for configs running over the tool-data/*.loc files thoughwhich is a pity. In the past we used a hack of the sy

[galaxy-dev] directory copies as zero-length file from job_working_directory?

Hi all, So I have a tool that I am writing a wrapper script for that produces a directory of images as one of its outputs. This directory gets created just fine in the job_working_directory, but then when the job finishes and the contents of the job_working_directory are copied, the copy of the i

Re: [galaxy-dev] inable to login to testtoolshed login because of Server Error: AttributeError: 'GalaxySession' object has no attribute 'current_history'

Jorrit, Thank you for the additional information, following those steps I was able to reproduce the error and will be looking into the issue. --Dave B. On 3/28/13 18:04:48.000, jorrit poelen wrote: Hey Dave, I just reproduced this issue by: 1. clear all cookies (reset browser) 2. login

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Jorrit, I've not been able to reproduce the first scenario using a local Galaxy instance against the test tool shed. Could you tell me which revision of Galaxy you're running when you encounter this behavior? I do see that the revision bb20766df19c that you were initially trying to update is

[galaxy-dev] list of tool versions and galaxy ami?

Hi all, Is there a canonical list of current tool versions that are running in the public galaxy? Is there a way to get that list? Also, I was hoping that there might be a galaxy ami that I could use in the amazon cloud and by that I mean NOT a cloudman instance. I am looking for an instanc

Re: [galaxy-dev] inable to login to testtoolshed login because of Server Error: AttributeError: 'GalaxySession' object has no attribute 'current_history'

Jorrit, While I investigate the root cause of this, have you tried clearing all cookies for testtoolshed.g2.bx.psu.edu? --Dave B. On 3/28/13 17:14:55.000, jorrit poelen wrote: Hey y'all galaxiers, Today, I tried to login using the testtoolshed web ui. To make sure that it wasn't just i

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Jorrit, I may have been a bit unclear in my previous response. Allow me to illustrate two scenarios: First scenario: 1. A repository is created containing a BWA tool with version 0.5.9 2. The repository is installed to Galaxy. 3. New README file is uploaded, tool version is *not* changed. Se

[galaxy-dev] inable to login to testtoolshed login because of Server Error: AttributeError: 'GalaxySession' object has no attribute 'current_history'

Hey y'all galaxiers, Today, I tried to login using the testtoolshed web ui. To make sure that it wasn't just isolated to an existing account, I created a new account, and still I encountered the Server Error attached below. This error is not shown when entering an invalid password. I was abl

Re: [galaxy-dev] upgrading cufflinks version to 2.0.2

> I am trying to upgrade cufflinks version from 1.3.0 to 2.0.2. I changed the > directory in the PATH to version 2.0.2 but when I run cuffdiff on the galaxy > it still uses the version 1.3.0. Do I need to change the code of the wrapper? This is the right approach, but there must be a glitch some

Re: [galaxy-dev] Toolshed - Installation of static files

Hello Lance, I've committed a fix for this issue into the next-stable branch on the galaxy-central repository in change set revision 9212:92c8a55a6679, so the fix will be included in the upcoming Galaxy release. This fix is currently running on both the test and main Galaxy tool sheds as well.

[galaxy-dev] Setting up SSL on CloudMan EC2

Has anyone configured SSL for nginx on CloudMan (AWS)? If so, can you share your nginx.conf file as I'm having some issues. *Details* I tried adopting the nginx.conf for CloudMan+CloudBioLiniux as described here

[galaxy-dev] Running with Multiple DRMs

Hi Galaxy-Dev, I have a new local instance that submits to cluster1 via pbs-drmaa-1.0.14. Galaxy is on a VM that is a submit node on cluster1, and there is a shared filesystem amongst all the clusters where the datasets are stored. The Galaxy VM is also a submit node on cluster2 and we have ins

Re: [galaxy-dev] Trinity wrapper not working on local installation

Hi, None of the solutions that were mentioned fixed the issue. I will do some more debugging later this evening. Thanks, Raj On Thursday, March 28, 2013 12:26:56 PM, James Taylor wrote: I haven't looked at this directly, but it should be using None, in which case the correct comparison is "l

Re: [galaxy-dev] Trinity wrapper not working on local installation

I haven't looked at this directly, but it should be using None, in which case the correct comparison is "library_type is None" and "library_type is not None". -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock wrote: > On Thu, Mar 28,

[galaxy-dev] negative user data usage

Hi, Today, I found out that one user in our local galaxy installation (the administrator user) has a negative disk usage. - Reports shows : -72780720701 bytes - Galaxy history shows: -1% Does anybody have suggestions on what might be causing this and how to solve it? There is about 660 Gb of

Re: [galaxy-dev] Knowing who is currently logged into your system

Hey Alex, Thanks for the quick response. The reason why I asked this question is because we reimplemented our plugin WS-Extension tool, which allows users to import web services as tools in Galaxy. This process involves making changes to tool_conf.xml, hence the restarting process is required.

Re: [galaxy-dev] Missing from tool shed - lost in migration or never uploaded?

On Thu, Mar 28, 2013 at 2:49 PM, Greg Von Kuster wrote: > Hi Peter, > > Everything that was in the pre-hg tool shed was moved to the new tool > shed - I don't remember any issues during that transition that would have > eliminated anything. I don't think there is anything retrievable from the > o

Re: [galaxy-dev] Missing from tool shed - lost in migration or never uploaded?

Hi Peter, Everything that was in the pre-hg tool shed was moved to the new tool shed - I don't remember any issues during that transition that would have eliminated anything. I don't think there is anything retrievable from the original tool shed at this point without some effort. You most li

[galaxy-dev] Missing from tool shed - lost in migration or never uploaded?

Hi Greg, Is there anything left of the old (pre-hg) Tool Shed? I'm wondering if I ever uploaded this tool back in early 2011, in which case could it have got lost in the migration to the current hg-based Tool Shed?: https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_primer_c

Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)

On Mar 22, 2013, at 4:57 PM, Lance Parsons wrote: > Nate Coraor wrote: >> >> On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: >> >>> I have been running a Galaxy server for our sequencing researchers for a >>> while now and it's become increasingly successful. The biggest resource >>> challe

Re: [galaxy-dev] Exporting histories fails: no space left on device

OK, it seems to be a proxy error. When the proxy does not receive data from the server, it times out, and closes the connection. I think the process that packs the datasets takes too long, so the connection is closed before the packaging is finished? Just a gues... From the httpd logs: =

Re: [galaxy-dev] Exporting histories fails: no space left on device

Hi Assaf, After all, the problem appears not to be total size of the history, but the size of the individual datasets. Now, histories which contain big datasets (>1GB) imported from Data Libraries causes the exporting process to crash. Can somebody confirm if this is a bug? I uploaded the d

Re: [galaxy-dev] Cancel running jobs/workflows through API

Richard, You can find the code for admin users stopping jobs in lib/galaxy/web/base/controllers/admin.py, in the jobs method of the Admin class. Hopefully that will provide the base structure for what you want to accomplish. --Dave B. On 3/27/13 12:02:20.000, Richard Park wrote: Hey guy

Re: [galaxy-dev] Trinity wrapper not working on local installation

On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam wrote: > Hello, > > I am trying to get the trinity wrapper to work on our local galaxy > installation using the latest trinity version. > > The main issue is that the Trinity.pl call has --SS_lib_type None in the > script file. The data I am using

Re: [galaxy-dev] Circster Visualization

It works!! I didn't know I have to save before to use circster!! Great!! Thanks a lot!! :D Stefania On 27/mar/2013, at 17:57, James Taylor wrote: > I think if you save your trackster visualization first then switching > over to circster should work fine. > > -- > James Taylor, Assistant Profes

Re: [galaxy-dev] Knowing who is currently logged into your system

Akshay If you have galaxy_reports running on your server you can see the most likely logged in users under: "Users/Date of last login" when you query it for 0 days. You at least have a login per day (not on the hour though). For restarting purposes we ignore "viewers" and monitor the running jobs

[galaxy-dev] Knowing who is currently logged into your system

Hi Akshay, I am going to post your question over to the galaxy-...@bx.psu.edu mailing list, to give it better viability. You could probably run an sql query against a database table to find out this information, but there may be a better way. Let's see if someone has a method worked out they

Re: [galaxy-dev] FTP upload - symlink to uploaded data

Hi Rob, Indeed, I had/have some difficulties with setting temporary directories. The problem was that FTP uploaded data was first copied to TMPDIR prior to being put in the database directory. My solution: I extended the /tmp partition to several GB's, by mounting a bigger device over it.