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BioGrids FAQ

Software version tracking in workflows

BioGrids software titles all have a version number associated with them. Most titles have more than one version available.

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How do I set the version to use?

Every title has a default version. You can change the version in use by using the version override environment variable for the title.

On Linux: export SAMTOOLS_X=1.9

On Mac: export SAMTOOLS_X=1.9

Details here: Overriding Software Versions

R version confirmation

From the command line, check your path:

$ R --sbwhich


$ which R

Use the biogrids-info utility:

$ biogrids-info -l r
  Version information for: /programs/i386-mac/r

Default version:                    3.3.2
In-use version:                     3.6.2

Installed versions:                 3.6.2
Other available versions:           3.6.2 3.5.1 3.4.2 3.2.1 3.2.2 3.0.3 2.13.0 2.11.1 
Overrides use this shell variable:  R_M

Check the version override variable:

$ echo $R_M

Within your R code:

> system("type R")
R is /programs/x86_64-linux/r/3.6.2/bin/R