Re: [galaxy-dev] cleanup

Dear Nicola, thanks it worked.  cheers, Philipp -Original message- From: Nicola Soranzo  Sent: Tuesday 23rd February 2016 20:35 To: Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] cleanup Hi Philipp, please alway reply to the mailing l

Re: [galaxy-dev] cleanup

Hi Philipp, please alway reply to the mailing list. I'm not using Docker, but if Galaxy is in the /galaxy-central/ directory and its version is 16.01, then: $ cd /galaxy-central/ $ . .venv/bin/activate $ python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -30 -1 $ deacti

Re: [galaxy-dev] correctly installing to toolshed

Hi Bjoern, it's stored in the same folder as the .xml Hi Gildas, that is the tool. Thanks! On Tue, Feb 23, 2016 at 12:43 PM, Gildas Le Corguillé < lecorgui...@sb-roscoff.fr> wrote: > Is it this tool : > https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_with_same_score/c

Re: [galaxy-dev] correctly installing to toolshed

Is it this tool : https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_with_same_score/c19a0a942e1b Gildas - Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for

Re: [galaxy-dev] correctly installing to toolshed

Hi, is the script rm_consecutive_sameScore.pl part of your TS repo and next to your tool XML file or where is it stored? Thanks, Bjoern Am 23.02.2016 um 17:46 schrieb Xianrong Wong: > Hi, I'm new to publishing tools/repository on the toolshed. I have used > planemo and lint and tests as well as

Re: [galaxy-dev] correctly installing to toolshed

Hi Gildas, thank you for the prompt reply! I actually have tried multiple paths to the script, even just the script name as you suggested but it's always giving the same error of "no such file or directory". On Tue, Feb 23, 2016 at 11:51 AM, Gildas Le Corguillé < lecorgui...@sb-r

Re: [galaxy-dev] correctly installing to toolshed

Hi, I think that you don’t need : .$__tool_directory__/ rm_consecutive_sameScore.pl "$input1" "$output1" seems enough if you join the script .pl with your wrapper .xml Gildas - Gildas Le Corguillé - Bioinformatician/Bioanalyste P

[galaxy-dev] correctly installing to toolshed

Hi, I'm new to publishing tools/repository on the toolshed. I have used planemo and lint and tests as well as serve all worked. I was able to use the tool. However, when I uploaded it onto the test tool shed and imported the tool on a cloud instance, I keep getting this error when running job:

Re: [galaxy-dev] cleanup

Hi Philipp, if you are using Galaxy release 16.01, you should load the virtualenv before running the cleanup script, e.g.: $ cd GALAXY_HOME $ . .venv/bin/activate $ python scripts/cleanup_datasets/cleanup_datasets.py ... Cheers, Nicola On 23/02/16 15:07, Hans-Rudolf Hotz wrote: Hi Philipp

Re: [galaxy-dev] cleanup

Hi Philipp point 1 : that's as expected - good. point 2 : looks like a docker specific issue? Maybe Bjoern can jump in? Hans-Rudolf On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote: Dear Hans-Rudolf, thanks a lot for your help. I did as you suggested: 1. when I go into the scripts

Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

On Tue, Feb 23, 2016 at 4:04 AM, Peter Cock wrote: > On Mon, Feb 22, 2016 at 9:02 PM, Nate Coraor wrote: > > On Mon, Feb 22, 2016 at 5:54 AM, Peter Cock > > wrote: > >> > >> Hi all, > >> > >> Last week at the Galaxy Admins video hangout Nate gave an > >> overview of the way Python dependency ha

[galaxy-dev] Docker and issue with shed_tool_conf.xml

Dear All,  I have a serious problem with installing new tools to our local Docker-galaxy-stable instance (latest version). All tools seem to install without any issue from the tool shed. When I check under Manage installed tools they all show a green "installed" button. However, the local

Re: [galaxy-dev] Docker and alpine linux

Just my 2 cents about this: I feel your pain, our connection to the docker hub is horrible, it takes an hour to pull the GIE images ... . (While it only takes seconds from the cloud ...). The galaxy docker images are pretty fat, because we use them VM-style, in principle nothing wrong about that. S

Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

On Mon, Feb 22, 2016 at 9:02 PM, Nate Coraor wrote: > On Mon, Feb 22, 2016 at 5:54 AM, Peter Cock > wrote: >> >> Hi all, >> >> Last week at the Galaxy Admins video hangout Nate gave an >> overview of the way Python dependency handling is changing >> from using egg files to using wheel files inste

Re: [galaxy-dev] Docker and alpine linux

Hi Tiago, thanks for the heads-up. I also tried alpine some time ago but Galaxy needs some external dependencies which Nate is building also with a ppa for Debian based systems. So this is not so easy to migrate. What we could do is to orchestrate the containers and its deps: https://github.com/