[galaxy-dev] I wrote a small script to reload tool pages

Hi, I wanted to reload xml tool wrapper pages without using the browser. Going off of this page... http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-March/009126.html I wrote a little python script that takes the tool name (the thing at the top of the xml wrapper file) as a parameter and reloads

Re: [galaxy-dev] Missing Tool Shed installation errors

Peter, This should be fixed in 10296:22fb05ea1b47, and clinod should no longer be in that list after the automated testing framework checks it again. --Dave B. On 8/2/13 09:56:25.000, Peter Cock wrote: Hi again, Currently under "Latest revision: installation errors' my clinod tool is lis

Re: [galaxy-dev] Jobs remain in queue until restart

I did some more investigation of this issue I do notice that my 4 core, 8 slot VM machine has a load of 32, with only my 4 handler processes running (Plus my web server), but not even getting more than 10% of the CPU each. There seems to be some process in my handlers that takes an incredible

Re: [galaxy-dev] shall us specify which tool run in cluster?

HI Shenwiyn, The definition of regularjobs etc. is there to allow each job to be run under different environment on the cluster. I am actually not using most of those definitions, except for the BWA tool, which I want to run using 4 slots on our cluster so I use the destination "multicorejobs4

Re: [galaxy-dev] Appending _task_%d suffix to multi files

Hi Jorrit, Thanks a lot for the explanation. Sorry to trouble on you holidays. Enjoy your time off. Cheers, - Piotr From: Jorrit Boekel [mailto:jorrit.boe...@scilifelab.se] Sent: Thursday, August 01, 2013 7:45 PM To: Szul, Piotr (ICT Centre, Marsfield) Cc: Khassapov, Alex (CSIRO IM&T,

Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS

On Wed, Jul 24, 2013 at 3:42 PM, Peter Cock wrote: > On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock wrote: >> On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster wrote: >>> Hello Björn, >>> >>> This one has been applied in changeset 10219:a7edac403b6c, and all of >>> your patches are now running on th

[galaxy-dev] account marked

Hi, I tried to login into my account today (cgkum...@gmail.com) and found that it has been marked for deletion. I have been doing some active analysis in that account, and the results have not been downloaded yet. When I had been notified about the account, I had indic

Re: [galaxy-dev] Tool Shed Tests failing with sniffer/ftype problem

Peter, As it turns out, the automated testing framework was not correctly handling the situation where dataset metadata is set externally. I've committed a fix for that in 10295:59243394031a, and this should result in seq_rename now being correctly tested. When it comes to the sniffer situat

[galaxy-dev] Printing the current date in a param value

Hello Is there a way to do something like this ? I would like to set a kind of default value to my param. ${time.strftime('%Y_%m_%d')} is not interpreted. I have tried this because it works within the label attribute in tag (for labeling my output) But it does not work for the label attribute

Re: [galaxy-dev] Choosing which nodes to run on for a whole history (Galaxy cluster)

On Jul 31, 2013, at 2:22 PM, Ben Gift wrote: > I'm setting up Galaxy and Torque with my cluster and I was wondering if I > could set it up so that nodes could be assigned for a whole history. This way > I can re-run histories on certain nodes for benchmarking runtimes. > > It seems that the cl

[galaxy-dev] Missing Tool Shed installation errors

Hi again, Currently under "Latest revision: installation errors' my clinod tool is listed on the Test Tool Shed, yet I don't see any errors displayed here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/deb6cb2db22b Any clues? Thanks, Peter __

Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

WoW ! Thats perfect ! Thank you very much !! :) On Fri, Aug 2, 2013 at 12:44 PM, Hans-Rudolf Hotz wrote: > and now, what happens, if you change it to 'tabular'? > > (click on the pencil icon - 'Edit Attributes', and then on Datatype > > ___

Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

and now, what happens, if you change it to 'tabular'? (click on the pencil icon - 'Edit Attributes', and then on Datatype On 08/02/2013 12:18 PM, Nikhil Mallela wrote: Hi Hans-Rudolf, I was wrong previously. It is output produced (.txt) while computing the quality statistics on the .qual fil

Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

Hi Hans-Rudolf, I was wrong previously. It is output produced (.txt) while computing the quality statistics on the .qual file The output format seems to have been detected by Galaxy as a ".txt" file. Here is a snapshot. [image: Inline image 1] Nikhil. On Fri, Aug 2, 2013 at 11:58 AM, Hans-Rudo

Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

Hi I guess, you misunderstood my question. I was revering to the format within galaxy, ie what is written in the preview window (unfortunately, you did cut this off from your pictures in your original post) between "format:" and ", database". Hans-Rudolf On 08/02/2013 11:50 AM, Nikhil Mall

Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

Hi Hans-Rudolf, The data format is ".qual" file from SOLiD sequencers. Its the same sample file that I've uploaded to the main and the local installation. But as you have seen in my previous post, the headers are inline with the data on main; but not on my local installation. what could be the rea

Re: [galaxy-dev] Toolshed repository update error

Hi Saskia, you need to fix that wrapper. Its a merge conflict you need to resolve by your own (indicated by << ==). Cheers, Bjoern > I am working on putting a tool into the toolshed. I have a bash script > wrapper. I uploaded the first version fine, but when I wanted to > upload a revisi

Re: [galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

Hi Nikhil what is the data format for this data set in your local installation and on main? Regards, Hans-Rudolf On 08/02/2013 09:56 AM, Nikhil Mallela wrote: Hi, A few days ago, I have installed the stable release of of Galaxy local instanceon my Workstation & I am running it behind Apa

[galaxy-dev] Toolshed repository update error

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<< local" etc strings are causi

Re: [galaxy-dev] Tool Shed Tests failing with sniffer/ftype problem

On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier wrote: > Peter, > > As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning > valid test results. Great - so this was a sniffer bug for the twobit format going wrong, https://bitbucket.org/galaxy/galaxy-central/commits/d34d6d1da813

Re: [galaxy-dev] Sudden error in local galaxy installation

After some investigating I think the problem is at the line: converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] in File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", lin

[galaxy-dev] How to get the data-view on local instance just like the Galaxy Main ?

Hi, A few days ago, I have installed the stable release of of Galaxy local instance on my Workstation & I am running it behind Apache web server proxy . In regard to the data snapshots, I've observed that, it is much more organized on the Galaxy main rather than on my local instance. For example,