Re: [galaxy-dev] Retrieve list of published workflows from API

Hey Phillip, I have looked through the API closely and I don't see a way to do this. I have created a Trello card for this. https://trello.com/c/LDm3dQvB Contributions welcome :). -John On Fri, Nov 1, 2013 at 12:24 PM, Philip Mabon wrote: > Is there a way to interact with the published workfl

Re: [galaxy-dev] Configurable toolshed package installation to support tool-dependency-resolver-plugins

Simon, As you have probably noticed a new stable galaxy was released. It includes 95% of what we discussed including this implicit check to see if tool shed packages are enabled. Your help implementing, testing, and driving these changes was greatly appreciated! I couldn't however pull the trigge

[galaxy-dev] Nov 04, 2013 Galaxy Distribution

Nov 04, 2013 Galaxy Distribution *usegalaxy.org* *CompleteNews Brief * *Highlights:* * A/*security vulnerability*/with filter tools trapped and fixed:*Upgrade o

Re: [galaxy-dev] latest galaxy-central version

I updated to the stable release and reproduced the issue. Step to reproduce 1. go to admin 2. Manage data libraries 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict a

[galaxy-dev] Security vulnerability in Galaxy filtering tools

A security vulnerability was recently discovered by John Chilton with Galaxy's "Filter data on any column using simple expressions" and "Filter on ambiguities in polymorphism datasets" tools that can allow for arbitrary execution of code on the command line. The fix for these tools has been com

Re: [galaxy-dev] latest galaxy-central version

Hello, I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation. --Marten On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch

Re: [galaxy-dev] Errors running DRMAA and PBS on remote server running Torque 4

Hi Alex, I should say that for the most part, our setup using Torque 4.x has worked. Under the following circumstances it has failed: 1.) When Torque configuration is changed but the pbs_server is not restarted 2.) When trying to route jobs to different clusters - the new cluster may work for ju

Re: [galaxy-dev] latest galaxy-central version

It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js W

[galaxy-dev] Question regarding walltime exceeded not being correctly reported via the WebUI

Hi, Galaxy Developers, I have what I hops is somewhat of a basic question regarding Galaxy's interaction with a pbs job cluster and information reported via the webUI. Basically, in certain situations, the walltime of a specific job is exceeded. This is of course to be expected and all fine and u

Re: [galaxy-dev] tool of installing tool shed repositories

Hello Ray and Björn, I'm currently working on the feature for importing a repository capsule into a Tool Shed. It's been on my plate for a while, but other priorities have side-tracked this work. Based on your exchange, I'm now working to finish up this feature, so it should be available in t

Re: [galaxy-dev] [galaxy-user] Inquiring

Hi Yan, As Hans mentioned, you should not need to update anything other than the `host` option in universe_wsgi.ini for most basic configurations (e.g. no proxy, database server (if any) is on the same server). Also, if you already have the host option set to 0.0.0.0, e.g.: host = 0.0.0.0

Re: [galaxy-dev] Galaxy dropping jobs?

Hi Nikolay, With slurm, the following change that I backed out should fix the problem: https://bitbucket.org/galaxy/galaxy-central/diff/lib/galaxy/jobs/runners/drmaa.py?diff2=d46b64f12c52&at=default Although I do believe that if Galaxy doesn't read the completion state before slurm "forgets"

Re: [galaxy-dev] Errors running DRMAA and PBS on remote server running Torque 4

Hi Carrie, It is a bug in Torque/4.x series. It can be fixed for a time by restarting the Torque pbs_server process, but it’s going to come back. It’s not galaxy-specific as any python-drmaa request will fail once Torque starts experiencing the issue. Regards, Alex From: , Carrie L mailto:cg

Re: [galaxy-dev] Supporting file sets for running a tool with multiple input files

Hi Pieter, We've worked out what we think is the right way to solve this for Galaxy and expect work to start soon. See the trello card ( https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more details. For your particular tool, the first workaround that comes to mind would be addin

[galaxy-dev] Supporting file sets for running a tool with multiple input files

Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool p

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

On Tue, Oct 22, 2013 at 10:43 AM, Peter Cock wrote: > On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier wrote: >> Peter, >> >> Thanks for the information, it uncovered a problem with the testing >> framework that has been resolved in 10817:6b0c3592dde1. The listed >> repositories should start showing

[galaxy-dev] Fw: Re: tool of installing tool shed repositories

ngsf...@hygenomics.com From: ngsf...@hygenomics.com Date: 2013-11-04 17:53 To: Björn Grüning Subject: Re: Re: [galaxy-dev] tool of installing tool shed repositories hi Bjoern: I am trying to bulk import repositories, by developing some tools following the thought similar to those in toolshed

Re: [galaxy-dev] tool of installing tool shed repositories

Hi Ray, there is some work in that direction to easily import and export repositories. The export feature is already integrated and should help you. You will end up with a tarball with all informations about that repository and the import should be easier. If you want to work on the import part, I

[galaxy-dev] tool of installing tool shed repositories

Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray ngsf...@hygenomics.com<<[5UQ[BL(6~BS2JV6(11-04-16