cfsan snp pipeline

Question

[saifulislam99121]

I am using cfsan_snp_pipeline. The link of the git is-

• https://github.com/CFSAN-Biostatistics/snp-pipeline

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.

[janejin]

I met the same problem as you. May I ask if you have solved this problem?

Answer 1

[Istvan Albert]

Sounds like the classpath is not exported into the shell.

https://www.baeldung.com/linux/bash-variables-export