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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

or 

$ 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
3.6.2

Within your R code:

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

Plan text before test table:

   

   

   

   

        body { font-family: Arial, sans-serif; margin: 20px; }

        table { border-collapse: collapse; width: 100%; margin-top: 20px; }

        th, td { border: 1px solid #ddd; padding: 8px; text-align: left; }

        th { position: sticky; top: 0; background-color: #f2f2f2; z-index: 1; }

        tr:nth-child(even) { background-color: #f9f9f9; }

        tr:hover { background-color: #ddd; }

        input[type="text"] { margin-bottom: 20px; padding: 10px; width: calc(100% - 22px); border: 1px solid #ccc; border-radius: 4px; }

   

Pkg	4.0.2	4.1	4.2.0	4.2.1	4.2.3	4.3.0	4.3.1	4.4.0
abind	Y	Y	Y	Y	Y	Y	Y	Y
acepack	Y	Y			Y	Y	Y	Y
ade4	Y	Y			Y	Y	Y	Y
affxparser	Y	Y			Y	Y	Y	Y
affy	Y	Y	Y	Y	Y	Y	Y	Y
affyio	Y	Y	Y	Y	Y	Y	Y	Y
aggregation		Y
airr	Y	Y			Y	Y	Y	Y
airway	Y	Y			Y	Y	Y	Y

Click Me

Plain text after test table.