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Question: Using module system with Galaxy
1
gravatar for binni
3.8 years ago by
binni • 20
Sweden
binni • 20 wrote:

Hi.

I have a local installation of Galaxy on our server. The server has a module system with loads of bioinformatics software and versions installed. Without galaxy we can load a module and execute the program so:

$ module load cutadapt/1.5.0

$ cutadapt a.fastq etc...

Can I somehow use these available tools, rather than install them through tool shed? It seems that installing through tool shed copies it's own binaries which it uses. 
slurm module galaxy • 1.1k views
ADD COMMENT • link •
modified 3.8 years ago by Wolfgang Maier • 600 • written 3.8 years ago by binni • 20
2
gravatar for Martin Čech
3.8 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

I assume the module system exposes the binaries on the PATH which should generally work with Galaxy. When installing tools from the TS there is an option _not_ to install its dependencies (whicih will avoid copying/compiling the binaries). However I think you have to make sure with every Galaxy Tool you want to use, that it will find the correct executable (in correct version) on its path when Galaxy wants to run it.
ADD COMMENT • link written 3.8 years ago by Martin Čech ♦♦ 4.9k
1
gravatar for Wolfgang Maier
3.8 years ago by
Wolfgang Maier • 600
Germany
Wolfgang Maier • 600 wrote:

In addition to what Martin said:

In the config/galaxy.ini main configuration file, there is an option

 

environment_setup_file

 

, which lets you specify a file to source before tools are run from Galaxy. I assume you could use this file to "module load" any specific tool versions that you want to activate for your users.
ADD COMMENT • link written 3.8 years ago by Wolfgang Maier • 600
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