Re: [galaxy-dev] Custom Builds not accessible for user

here -- I'll get a fix out shortly. -Dannon On Mon, Dec 8, 2014 at 7:23 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear Galaxy Dev One of our users has managed to lock himself out of his Custom Builds. An 'Internal Server Error' appears and this shows up in the web process log

Re: [galaxy-dev] Egg distribution error

Hi all For what it's worth, I manually installed mock (and pycrypto because that was the next thing it complained about) and it worked after that. Ulf On 14/01/15 14:23, Ulf Schaefer wrote: Hi all After the announcements this morning, I upgraded to the latest stable release as suggested

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

> > python > > > And you have to include tool_dependencies.xml file which will look > something like: > > > > > prior_installation_required="True" /> > > > > Please let me know if you have more questions. > > M. > > On Tue, Dec 1, 20

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

18d3d >> >> You will need to add to your wrapper's xml something like: >> >> >> python >> >> >> And you have to include tool_dependencies.xml file which will look >> something like: >> >> >> >> >> > p

[galaxy-dev] Publish tool with Python dependencies to the toolshed

(to me). Thanks for any pointers and sorry if this has been answered some place I did not look. Cheers Ulf -- Ulf Schaefer, PhD Bioinformatics Scientist Bioinformatics Unit - Infectious Disease Informatics National Infection Service Public Health England 61 Colindale Ave, London NW9 5EQ ulf

Re: [galaxy-dev] This job failed for reasons that could not be determined.

randomly with any > tool? or are they all coming from the same tool? > > > Regards, Hans-Rudolf > > > > > On 07/25/2016 12:48 PM, Ulf Schaefer wrote: >> Hi all >> >> Certain jobs fail on my cloud Galaxy instance with the error message in >> the subject

[galaxy-dev] default number of concurrent jobs

Hi all I installed an out-of-the-box Galaxy instance on my local machine as per the instructions (https://wiki.galaxyproject.org/Admin/GetGalaxy). I have made minimal adjustments beyond making myself an admin. When I run a workflow in batch mode on 10 data sets it appears to running 5

Re: [galaxy-dev] default number of concurrent jobs

> > https://wiki.galaxyproject.org/Admin/Config/Jobs > > > Regards, Hans-Rudolf > > > > On 07/14/2016 01:35 PM, Ulf Schaefer wrote: >> Hi all >> >> I installed an out-of-the-box Galaxy instance on my local machine as per >> the instructions (https://

Re: [galaxy-dev] Metadata setting python dependencies

: Hi Ulf, you can set a virtualenv to be used in your job_conf.xml file. The following line would go into the `` tag: `` Best, Marius On 25 October 2017 at 16:56, Ulf Schaefer <ulf.schae...@phe.gov.uk <mailto:ulf.schae...@phe.gov.uk>> wrote: Hi again Update, sorry

[galaxy-dev] Metadata setting python dependencies

python version from the virtual env. Needless to say I can import json just fine using that python version. Any ideas? Any help is greatly appreciated. Thanks Ulf -- Ulf Schaefer, PhD Bioinformatics Scientist Bioinformatics Unit - Infectious Disease Informatics National Infection Service Publ

Re: [galaxy-dev] Metadata setting python dependencies

ug 9 2016, 06:11:56) [GCC 4.4.7 20120313 (Red Hat 4.4.7-17)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import json >>> Does anyone have an idea how I can stop this from happening? Where is th

Re: [galaxy-dev] Metadata setting python dependencies

October 2017 at 18:24, Ulf Schaefer <ulf.schae...@phe.gov.uk <mailto:ulf.schae...@phe.gov.uk>> wrote: Hi Marius This is very useful, but not quite there. I use in my job_conf.xml /this/is/a/test and I end up with this PATH=/phengs/hpc_