Version Management for Software Titles

Documenting versions of software used in workflows is critical for reproducibility.

BioGrids provides several versions for most software titles. The version in use can be set explicitly using a version override variable. See Overriding Software Versions for details.

Below we provide details for automatic version logging and activating previous versions.

Automatic Logging

BioGrids provides an environment variable for logging all BioGrids executable activity.

The environment variable “SBCAP_METRICS” can be set to either FILE or BOTH in this form:

FILE | FILE:path/to/file

BOTH | BOTH:path

When set to FILE (either form) logging is written to a FILE.

If no path to file is given then the default is $(HOME)/${GRID}capsule_log${HOSTNAME}.

When set to BOTH|BOTH:path logging is sent to a file as above and also to BioGrids servers. Capsule activity sent to BioGrids is deidentified and encrypted.

Sample Entries in the log file have this form:

2021-09-20T07:32:00EDT jjv5 M1-Air BIOGRIDS osx-11.2.1 biogrid-production_2.4.0 newrc_sh 4AADF0D0-3ADF-43EE-BD7E-6DCA9C85A627 NONE:samtools 0:22208 /programs/i386-mac/samtools/1.13/bin/samtools 1 3 

The path to the executable provides the architecture, name of the BioGrids title, version used and name of the executable called.

Finding Available Versions

The biogrids-info tool can be used to list all available versions of a title whether they are installed on your platform or not.

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

Default version:                    1.13
In-use version:                     1.13

Installed versions:                 1.13
Other available versions:           1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 
Overrides use this shell variable:  SAMTOOLS_M

Activating Older Versions

If you need to use a non-default version of a title you can specify this version with an override variable ( see Overriding Software Versions for details).

If the version of a title is not available on your platform you can install that version by specifying it either in the BioGrids GUI Installer or on the command line:

./biogrids-cli install samtools@1.7

BioGrids versions are retained for every title. We do not delete or remove versions of any title. If you are unable to find the version you need or have difficulty installing, please send a note to help@biogrids.org.

Using older R packages

Since Janurary 2020, BioGrids maintains all versions of R packages that have been installed in thet latest BioGrids R.

When new packages are installed or updated the previous set of packages is marked obsolete and archived. This happens approximately once per month.

You can use these older versions of R packages by requesting the obsolete package archive. Send email to:

help@biogrids.org

specifying either a specific version of an R package or the date you were using the version. We will restore the set of R packages that contains the version you need.

Once updated on your site you can use these older R packages by specifying them in your .libPaths() within R.

The path to R library packages in BioGrids is of the form:

/programs//x86_64-linux//r/3.6.2/r-pkgs/20200305

This path refers to R version 3.6.2 with a package directory named with a date: 20200305

To use packages from this directory, load the path using the .libPaths() function:

>.libPaths("/programs//x86_64-linux//r/3.6.2/r-pkgs/20200305")

Packages found in this directory will be loaded first.

To verify a package version use the packageVersion() funtcion.