Install python/pip/aws cli instead of using the installer, because -merge needs to run serratus_summarizer.py
Copy over samtools
Clean up some random quoting in run_merge.sh
I wasn't able to get anything to run, because I couldn't find a valid configuration for the scripts. I kept running into an error about a missing .sumzer.tsv. It looks like that's built from the $JOB_JSON, so I tried setting it to export JOB_JSON='{"genome":"flom2"}', because I found a flom2.sumzer.tsv in the right place in s3, but it still didn't work.
If anyone has a suggestion I can run from my machine to verify I can keep working on it, or if its easier you guys could run/verify.
This one will bring merge in line with -align and -dl
-mergeneeds to runserratus_summarizer.pyrun_merge.shI wasn't able to get anything to run, because I couldn't find a valid configuration for the scripts. I kept running into an error about a missing
.sumzer.tsv. It looks like that's built from the$JOB_JSON, so I tried setting it toexport JOB_JSON='{"genome":"flom2"}', because I found aflom2.sumzer.tsvin the right place ins3, but it still didn't work.If anyone has a suggestion I can run from my machine to verify I can keep working on it, or if its easier you guys could run/verify.
This one will bring merge in line with
-alignand-dl