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CFSAN-Biostatistics / snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
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classpath configuration error #23

Closed saifulislam1997 closed 2 years ago

saifulislam1997 commented 2 years ago

I have installed all the dependencies and install the pipeline via conda. when I execute the command- echo $CLASSPATH

/home/saiful/home/saiful/Downloads/picard-2.18.2.jar:/home/saiful/home/saiful/Downloads/VarScan.v2.3.9.jar:/home/saiful/home/saiful/Downloads/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar:

when I run the pipeline, cfsan_snp_pipeline run genomic.fasta -o cfsan_pipeline -s listeria
Checking dependencies... CLASSPATH is not configured with the path to VarScan.jar Error: Unable to access jarfile /home/saiful/home/saiful/Downloads/picard-2.18.2.jar

Error: Unable to access jarfile /home/saiful/home/saiful/Downloads/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar

Check the SNP Pipeline installation instructions here: http://snp-pipeline.readthedocs.org/en/latest/installation.html

I have checked the path and everything is fine in my sense. Can you help me? It is an urgency.

Thank you.