[galaxy-dev] Load tools without service interruption

Hi Galaxy team, Is there a way to add a tool without service interruption ? Something like a "sh run.sh --reload" (not "restart") command. I think I saw this information once, but I can't put my hand on it anymore. Thanks in advance ! F.T __

[galaxy-dev] Galaxy External Authentication and API access

I am currently using Apache and CAS (https://en.wikipedia.org/wiki/Central_Authentication_Service) to provide external authentication to Galaxy. I'd like to start using the API, however, I've not been able to find a way to get that to work. A while back, someone suggested using the following:

Re: [galaxy-dev] Alternative methods for external authentication

Hi Amelia, The authentication system was re-worked within the past year to a pluggable module system. There is a reference LDAP implementation that does not use Apache at all, as well as a few other examples li

[galaxy-dev] Alternative methods for external authentication

I'd like to set up a galaxy instance to use a custom external authentication system. The documentation has examples of using LDAP and Apache-based authentication, but I wondered if there was a more general method for hooking up a login system. Thanks! Amelia Ireland Integrated Microbial Genomics

Re: [galaxy-dev] Missing modules after upgrade to 16.01

Hi Cristian, It's up to you whether you keep it with Galaxy or not. I prefer not to modify the Galaxy clone at all so I keep it outside. More details about keeping the virtualenv separate can be found here in the documentation: https://docs.galaxyproject.org/en/master/admin/framework_dependencie

Re: [galaxy-dev] Missing modules after upgrade to 16.01

Hi Bjoern, Thanks for the tip! My problem was that galaxy assumes that the venv is in the installation directory as a hidden folder whilst I have the virtual environment installed at ~/venv and configured in my .bashrc to launch at login. Why I installed it like that? I don't remember... Probabl

[galaxy-dev] Galaxy 15.10 Jobs not running

Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file. I see in github, commits have recently been made to revert something, but I'm not clear what. Is there something going on wit

Re: [galaxy-dev] Python 2.6 Support

Thanks John, We're having some teething issues apparently due to using Python 2.7 on a system default of Python 2.6, but I have no real objection to these plans for dropping Python 2.6 support. http://dev.list.galaxyproject.org/Dependencies-for-sudo-scripts-drmaa-external-runner-py-tt4668988.html

Re: [galaxy-dev] Python 2.6 Support

Given there have been no objections and the 16.01 release notes contained a deprecation note and no one has complained - I just wanted to follow up on this thread with the announcement that 16.01 will be the last release of Galaxy to support Python 2.6. Likewise the next releases of pulsar and plan

[galaxy-dev] March 2016 Galaxy News: GCC2016 deadlines this month, GSOC 2016, RAD-Seq Hack …

Hello all, The *March 2016 Galactic News * is hot off the presses: - *GCC2016 * news: - *Oral presentation abstracts due March 20

Re: [galaxy-dev] tmp directory

Hi, Does this method is still valid : https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets ? Here is what I used (not anymore; in a cron): &<-&< #!/bin/bash # purge galaxy datasets, histories, folders, libraire

Re: [galaxy-dev] tmp directory

You can use tmpwatch on RedHat/CentOS/Fedora or tmpreaper on Debian/Ubuntu. Cheers, Nicola On 01/03/16 14:30, Raphenya, Amogelang wrote: Is there a script that is used to clean up database/tmp / / /*Amos Raphenya* / /Bioinformatics Software Developer/ /Department of Biochemistry & Biome

Re: [galaxy-dev] tmp directory

Is there a script that is used to clean up database/tmp Amos Raphenya  Bioinformatics Software Developer Department of Biochemistry & Biomedical Sciences McMaster University, MDCL 2317 p: (905) 525-9140 ext: 22787 a: 1280 Main St W.,Hamilton, Ontario, Canad

[galaxy-dev] workflows "show in menu" by default

Hi all, In the /workflow/configure_menu screen there is an tickbox option for each installed workflow to "show in menu". Is there a way I could enable this by default, or in code via bioblend (couldn't see any hint of this in the docs)? Perhaps I could extend bioblend to do this? Cheers, C

Re: [galaxy-dev] GATK problems with data manager

Hi Scott, as far as I know the GATK wrappers > 3.4 are community maintained, there is not much we can do for you here. I personally stopped to work on GATK because of the license issues and all I know is that the iuc/devteam datamanager worked for GATK2.8. Sorry, Bjoern Am 01.03.2016 um 13:52 s

[galaxy-dev] GATK problems with data manager

Hi all, Sorry to be repetitive, but this issue is really blocking our efforts to develop the workflow that we need in our instance of Galaxy. If anyone has any familiarity with the issue described below, please let me know. I really need to get this solved. One of my co-administrators is having s

Re: [galaxy-dev] Missing modules after upgrade to 16.01

Hi, please have a look at this script and run it: ./scripts/common_startup.sh Also make sure you have samtools installed. Ciao, Bjoern Am 01.03.2016 um 13:39 schrieb C. Ch.: > Hi, > > I've upgraded to 16.01 and have error messages indicating missing > modules. This produces problems while set

[galaxy-dev] Missing modules after upgrade to 16.01

Hi, I've upgraded to 16.01 and have error messages indicating missing modules. This produces problems while setting the metadata. The processes run, the results are there but the history entry is in red. How can I trigger the installation of all the modules that galaxy needs with the new pip bas

[galaxy-dev] novoalign in Galaxy

Hi there We're busy integrating novoalign in our local Galaxy - there doesn't seem to be a tool around for this, but I recall some people saying they were using (single threaded) novoalign with Galaxy. Does anyone know if tool XML has already been written? If not, we'll just have to write it. Pet

Re: [galaxy-dev] Downgrade tool upload tool

Thanks a lot Peter and Aysam! The fix worked perfectly! Regards, Makis Date: Mon, 29 Feb 2016 22:18:37 -0500 Subject: Re: [galaxy-dev] Downgrade tool upload tool From: aysam.guer...@gmail.com To: p.j.a.c...@googlemail.com CC: makis4e...@hotmail.com; j...@galaxyproject.org; galaxy-...@lists.bx.ps