Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Eric Kuyt
Hi Anna, Setting your own path variables shouldn't be necessary for toolshed tools, so probably something is wrong with the installation. could you post your tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log file? On 26 November 2014 at 13:49, Anna

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Eric Kuyt
​Could you try going to Admin - Manage Installed tool shed repositories uninstall - reinstall ​package_samtools_0_1_18 On 26 November 2014 at 16:55, Anna Terry iseegl...@googlemail.com wrote: yway, I am also getting the problem with samtools filter sam or bam -- Central Veterinary

[galaxy-dev] Reasons to choose psql over mysql or not

2015-07-27 Thread Eric Kuyt
Hi All, We are thinking of putting our galaxy instance in a new more powerful environment. Galaxy is now on a single server containing a psql database which is migrated from mysql a few years ago. The new environment already houses a really nice backupped highly available mysql server. as galaxy

Re: [galaxy-dev] Reasons to choose psql over mysql or not

2015-07-27 Thread Eric Kuyt
/27/2015 02:35 PM, Eric Kuyt wrote: Hi All, We are thinking of putting our galaxy instance in a new more powerful environment. Galaxy is now on a single server containing a psql database which is migrated from mysql a few years ago. The new environment already houses a really nice

[galaxy-dev] init scripts version 16.01

2016-03-19 Thread Eric Kuyt
Hey guys, today I updated to the latest version of galaxy. No I noticed that because of the new virtualenv/wheel startup procedure, the init scripts as mentioned here https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29 are not working anymore. Whet is the new

Re: [galaxy-dev] init scripts version 16.01

2016-04-11 Thread Eric Kuyt
. But this woudn't make me very happy. in File: /lib/galaxy_ext/metadata/set_metadata.py a sys.path.insert to .venv/lib should be added. I don't know what the right plcae for this is. Do you hava any better ideas for this matter? Eric On 8 April 2016 at 16:15, Eric Kuyt <eric.ku...@wur.nl>

Re: [galaxy-dev] init scripts version 16.01

2016-04-02 Thread Eric Kuyt
are not working anymore. What is the new startup procedure? I kind of dislike galaxy changing to virtualenv and not change your documentation and not answering my question. On 17 March 2016 at 14:00, Eric Kuyt <eric.ku...@wur.nl> wrote: > Hey guys, today I updated to the latest version of gal