CHARLIE: Circrnas in Host And viRuses anaLysis pIpEline

Published November 25, 2024 | Version v0.11.1

Software Open

1. Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA

CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
Update docker containers to set $PYTHONPATH. (#119, #125, @kelly-sovacool)
- Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with -C.
- Also use python -E to ensure the $PYTHONPATH is not carried over. (#129, @kelly-sovacool)
Fix reconfig to correctly replace variables in the config file. (#121, @kelly-sovacool)
Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
Fix missing output files due to file system latency and use real (absolute) paths where possible. (#130, @kelly-sovacool)
Update documentation to reflect biowulf usage and improved test dataset. (#132, @kelly-sovacool)

Notes

Please cite CHARLIE as below.

Name	Size	Download all
CCBR/CHARLIE-v0.11.1.zip md5:aba5696acceead467246573d2fba61ed	133.3 MB	Preview Download

Is supplement to: Software: https://github.com/CCBR/CHARLIE/tree/v0.11.1 (URL)