I am trying to run Picard in Singularity and try as I might I cannot seem to find the path to use. For example with GATK 220.127.116.11 I use the following path:
singularity exec $singularity_image /gatk/gatk --java-options -Xms8000m \
singularity_image is a variable that encodes the path to the gatk.sif. However, I cannot seem to figure out the path I need to use for picard.
When I look inside the Singularity file with the following code:
singularity exec picard_latest.sif /bin/bash -c "ls /"
I get the following:
bin boot dev environment etc home lib lib32 lib64 libx32 media mnt opt proc root run sbin singularity srv sys tmp usr var
Attempt 1: Using Find
singularity exec picard_latest.sif find / -name "picard.jar" 2>/dev/null
However, this gave no results.
Attempt 2: Going Down The Opt Path
singularity exec picard_latest.sif /bin/bash -c "ls /opt/"
This led to a file called
java and that had only one file in it called
openjdk so that seemed to be where java was stored.
Attempt 3: Looking In Boot
singularity exec picard_latest.sif /bin/bash -c "ls /boot/"
This yielded no results as it seems to be an empty file.
I have made other attempts but I cannot seem to establish the path I should use. I cannot change the java directly as it is preset on my cluster.
Does anyone know what the path would be for the latest version of Picard or could point me to how to look for this as I cannot seem to find this?