Error in running

[baoyl818]

Dear friend:

I have successfully installed the software, but when I run the pipeline with the following command line:

pipeline="/work/Software/STRetch-master" bampath="/work//bam" $pipeline/tools/bin/bpipe run $pipeline/pipelines/STRetch_exome_bam_pipeline.groovy $bampath/A.recaled.bam $bampath/B.recaled.bam $bampath/C.recaled.bam $bampath/D.recaled.bam

The error occurs : Error: Could not find or load main class org.codehaus.groovy.tools.GroovyStarter

I have installed groovy , but this error still happens . can you please tell me how to solve it ? Thanks very much Best

[hdashnow]

Hi @baoyl818, Thanks for reporting this. Let me see if I can replicate the error, and I'll get back to you. Warm regards, Harriet

[hdashnow]

Would you mind running the install test to see if that works? https://github.com/Oshlack/STRetch/wiki/Installing-STRetch