[galaxy-dev] October 2014 Galaxy Newsletter

2014-10-01 Thread Dave Clements
Hello all, A lot is happening in in the Galaxy in October, and a lot of good stuff happened in September too. Take a look at the October 2014 Galaxy Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_10 for the complete story, but here are some highlights: - *Galaxy needs your

[galaxy-dev] Get Data - url upload (connection timed out)

2014-10-01 Thread Elizabeth Chia
Dear * I have a local galaxy instance installed on a cluster. I've been trying to upload data by URL but kept getting this error: *unable to fetch url of data [Errno socket error] [Errno 110] connection timed out. *I've tried with and without file compression format and still gives me that

[galaxy-dev] bowtie_indices.loc for 'bowtie_wrappers' tool

2014-10-01 Thread Peter Briggs
Dear all Am I right in thinking that, although the current 'bowtie_wrappers' package from the toolshed creates the file .../galaxy-dist/tool-data/bowtie_indices.loc no data is ever actually loaded from this file (and so any entries added to it are ignored)? Empirically, it appears

Re: [galaxy-dev] Internal Server error when attemptng to use Admin Tab

2014-10-01 Thread John Chilton
Hello David, We don't have a workaround yet - but we (Dan did most of the investigating) understand the problem I think. You are using a MySQL database I assume? (Ignore the rest of this e-mail if not). I think MySQL has lower limits on the size of BLOBs that can be stored in the database than

Re: [galaxy-dev] Get Data - url upload (connection timed out)

2014-10-01 Thread John Chilton
I doubt there is a config option somewhere that is going to fix this. Can your compute nodes download external data outside of Galaxy? (One could submit a test script to the cluster with a download and see if it succeeds.) If you give me the URL and let me know what kind of cluster you are

Re: [galaxy-dev] Login with a system user

2014-10-01 Thread John Chilton
I don't know how one would do this precisely but I believe it is possible at the proxy level - i.e. setting up Apache to handle this and authenticate with system resources. I believe Tim Booth's work on integrating galaxy into biolinux uses system users for authentication by default. The

Re: [galaxy-dev] 'KeyError' in workflow extraction when using newer tool version

2014-10-01 Thread John Chilton
Sorry this has been sitting in my inbox for a while - because I wanted to try to fix it before the next release but I don't think it is going to happen. Generically - it doesn't surprise me that Galaxy can handle certain parameters changing between versions but not conditionals - they are handled

Re: [galaxy-dev] Simple standard for API use of a global user/key that all loaded tools can draw upon?

2014-10-01 Thread John Chilton
I don't know about a standard way of doing - I am not sure about Galaxy officially supporting this but you can add whatever properties you want in universe_wsgi.ini (which will be renamed config/galaxy.ini in coming release). These can be accessed within tool cheetah blocks as

Re: [galaxy-dev] Login with a system user

2014-10-01 Thread Will Holtz
This should be possible with Apache as the proxy and the mod_auth_pam Apache module. From a high level, the configuration should be similar to using mod_authnz_ldap or mod_auth_kerb as documented here: https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases -Will On Wed, Oct 1, 2014 at

[galaxy-dev] Vagrant-Galaxy for development purposes

2014-10-01 Thread Kandalaft, Iyad
Hi Everyone I wanted to share some code with the galaxy community and I am looking for opinions on the following approach. Overview: We want to create a standardized galaxy tool development environment to address specific problems we faced in the past while minimizing training and

[galaxy-dev] Jobs stuck in new state - Data Library datasets to blame?

2014-10-01 Thread Lance Parsons
Recently, I updated our Galaxy instance to use two processes (one for web, the other as a job handler). This has been working well, except in a few cases. I've noticed that a number of jobs get stuck in the new status. In a number of cases, I've resolved the issue by downloading and

Re: [galaxy-dev] Jobs stuck in new state - Data Library datasets to blame?

2014-10-01 Thread Aaron Petkau
Are you attempting to upload datasets to a Data Library, and then copy to a history and run jobs on them right away? I've run into issues before where if I attempt to run a job on a dataset in a library before it is finished being uploaded and processed, then the job gets stuck in a queued state