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:

hostname BIOGRIDS osx-10.13.6 biogrid-production_1.0.695 newrc_sh CA5BBF5F-F41E-4CFA-8AA4-37182C9DD366 /programs/i386-mac/samtools/1.10/bin/samtools 0 0
hostname BIOGRIDS osx-10.13.6 biogrid-production_1.0.695 newrc_sh 3355483F-A04B-4575-868F-88D22173C957 /programs/i386-mac/python/3.6.5/bin/python 0 0

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/x86_64-linux/samtools

Default version: 1.10

In-use version:  1.10

Installed versions:  1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19

Other available versions:  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_X

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 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.