I have been trying to get lumpyexpress to work on a bovine sample. Initially based on previous posts I thought it was a make error caused by missing -lcrypto however after installing openSSL the make error went a way however I am still not getting any output. (There are a few warnings) Below is my path and cmd being called. If there is any more information that would be helpful in puzzling out why lumpyexpress isn't giving any output would be greatly appreciated!
Hi -
I have been trying to get lumpyexpress to work on a bovine sample. Initially based on previous posts I thought it was a make error caused by missing -lcrypto however after installing openSSL the make error went a way however I am still not getting any output. (There are a few warnings) Below is my path and cmd being called. If there is any more information that would be helpful in puzzling out why lumpyexpress isn't giving any output would be greatly appreciated!
PATH=/var/lib/condor/execute/slot1/dir_25813/lumpy-sv/bin:/var/lib/condor/execute/slot1/dir_25813/program_bin:/var/lib/condor/execute/slot1/dir_25813/samblaster:/var/lib/condor/execute/slot1/dir_25813/openSSL/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/opt/puppetlabs/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/blett/.local/bin:/home/blett/bin
cmd = lumpyexpress -B JERUSAM000000654500_dedup_recal.bam -o TEST