rienv
Author: Sean Maden
Programmatic setup for retained intron detection tools with conda
. This resource currently
supports environment setup for the following tools:
Make environments
Run the shell script conda.sh
:
sh conda.sh
Alternatively, set up environments from their .yml
files, located at ./inst/yml/
:
conda env create -f ./inst/yml/env_interest.yml
Tests
Scripts to test environments, especially using any provided vignette examples, are contained at ./inst/test
.
Cross-tool tests
The test BAM files provided by the IntEREst
package are contained in the folder ./inst/bam
. These consist of
a small example BAM .bam
and BAM index .bai
file aligned with hg19. The example BAM data was used to test
each of the retained intron tools, where scripts and test results are contained at ./inst/bam/tests/tooltests/
.