Default output directory cannot be modified about tetools HOT 3 CLOSED

It's the same issue with RepeatModeler

singularity exec instance://repeatmodeler RepeatModeler -database ${SPECIES} -pa ${SLURM_CPUS_ON_NODE} -LTRStruct

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Describe the bug
Hi,

I cannot change the default output directory when mounting the image in singularity. It will always write to home. There should be an option to specify the output directory and/or the working directory. LOCAL is the local scratch directory. Even though I specifically try to overide the home directory, it will always write to the home directory. Please advice

This doesn't sound right: by default, BuildDatabase and RepeatModeler should both write their output to the current working directory.

To Reproduce

CWD=$(pwd)
cp repeatmodeler.sif ${LOCAL}
cp ${MYFASTA} ${LOCAL}
cd ${LOCAL}

export HOME=${LOCAL}
HOME=${LOCAL}
MOUNTDIR=/data
singularity instance start --bind $(pwd):${MOUNTDIR} repeatmodeler.sif repeatmodeler

SPECIES=myspecies

singularity exec instance://repeatmodeler export HOME=${MOUNTDIR}
singularity exec instance://repeatmodeler BuildDatabase -name ${SPECIES} ${MOUNTDIR}/$MYFASTA

singularity instance looks unnecessary for this task since there is no process that needs to be run in the background; is there some other advantage to it? It is difficult for me to follow along and guess which variables or working directories will be set when using instance, and that singularity exec export command is incorrect. This simpler script should be able to accomplish the same, without singularity instance:

cp repeatmodeler.sif ${LOCAL}
cp ${MYFASTA} ${LOCAL}/genome.fa
cd ${LOCAL}

SPECIES=myspecies

singularity exec repeatmodeler.sif BuildDatabase -name ${SPECIES} genome.fa
singularity exec repeatmodeler.sif RepeatModeler -database ${SPECIES} -pa ${SLURM_CPUS_ON_NODE} -LTRStruct

By default singularity exec should mount the current directory and run the program there, and both BuildDatabase and RepeatModeler will write to it. If that doesn't work, for example if you have a different system configuration that doesn't mount the current directory by default, I recommend trying the --bind, --env, and/or --pwd options manually (instead of singularity instance).

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Closing due to inactivity. Please feel free to re-open or open a new issue if you have further problems or questions!

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