singularity image based on MGI stLFR docker image(https://github.com/MGI-tech-bioinformatics/stLFR_V1.3).
As the MGI provides stLFR docker images. But it is difficult to run docker container on HPC clusters. Singularity provides a solution to run container on HPC. So I convert the stLFR docker image to singularity image.
this folder contains the def file to build singularity image. You can use it to build your own singularity image with singularity build -f <stLFR.sif> <stLFR.def>。
Please do not override folders /perl5, /stLFR as they contain necessary files.
When you successfully build a sif file(singularity image format), for example the stlfr_v1.3.sif, here is a simple example on how to use it.
db="/path_to_stlfr_db"
data="/path_to_data"
result="/path_to_result"
sif="stlfr_v1.3.sif"
name="test"
singularity exec \
-B ${db}:/stLFR/db/ \
-B ${data}:/data \
-e \
${sif} \
/bin/bash \
/stLFR/bin/stLFR_SGE \
${result}/samples.list \
${result} >${name}.stLFR.log 2>&1I just clean the env using -e in case you set some wrong environment variables.
Please note this is just a shell command, and it may run for a long time.
You can find all the things from MGI GitHub: https://github.com/MGI-tech-bioinformatics/stLFR_V1.3.
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