https://github.com/CFSAN-Biostatistics/snp-pipeline
Tip revision: 065e93a7d966c8534b77b6d9de26dd350cebc35d authored by Justin Payne on 05 May 2023, 03:45:32 UTC
bugfixes, trying to improve Conda support
bugfixes, trying to improve Conda support
Tip revision: 065e93a
environment.yml
name: snp-pipeline
channels:
- bioconda
- conda-forge
dependencies:
- snp-pipeline
- bowtie2
- smalt
- samtools
- picard==2.18.11
- varscan==2.4.4
- tabix
- bcftools
- gatk==3.8
post_activate:
- export CLASSPATH=$CONDA_PREFIX/share/picard-2.18.11-0/picard.jar:$CONDA_PREFIX/share/varscan-2.4.4-1/VarScan.jar:$CONDA_PREFIX/opt/gatk-3.8/GenomeAnalysisTK.jar