[BUG] TD2.LongOrfs: not found when running SQANTI3 v6.0.1 from singularity (docker) container

[skudashev]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Are you running SQANTI3 on its latest release?

• I have SQANTI3 updated to the latest release

Problem description

I tried installing SQANTI3 v6.0.1 using singularity build sqanti3_6.0.1.sif docker://anaconesalab/sqanti3:v6.0.1, the build worked fine but when trying to run sqanti3_qc.py it does not find TD2.LongOrfs. I cannot load the conda environment as we no longer use conda and hoped that the docker image would contain all dependencies.

Code sample

singularity exec --cleanenv sqanti3_6.0.1.sif \
  /conda/miniconda3/envs/sqanti3/bin/python \
  /opt2/sqanti3/6.0.1/SQANTI3-6.0.1/sqanti3_qc.py 

Error

/bin/sh: 1: TD2.LongOrfs: not found

Anything else?

Looks like the container image does not set an ENV PATH in its Dockerfile, so neither TD2.LongOrfs or Rscript or others are exposed or added to PATH

[Fabian-RY]

Hi @skudashev

When using "exec" to run the script in the container, it does not load the conda environment by default. In the FAQ of the installation for docker) , we recommend to use "singularity run", as the entrypoint is configured to activate the conda environment before running Sqanti3. It is explicitly noted that exec won't load it by default.

As you are trying to run the python executable (from the conda environment) but not loading the conda environment, environment variables are not set up, and therefore, fails to find the binaries of the tools.

You should either:

• Use Singularity run sqanti3_6.0.1.sif sqanti3_qc.py (which is the recommended way), which will load the environment before executing your script
• If you really need to use exec, and cannot use run, call the conda environment before executing with (singularity exec sqanti3_6.0.1.sif conda run -n sqanti3 sqanti3_qc.py)

[skudashev]

Hi @Fabian-RY

I see, thank you for clarifying. As I use SQANTI3 within a Nextflow pipeline, Nextflow itself uses singularity exec rather than run so I couldn't really change that.
Adding --env PATH=/conda/miniconda3/envs/sqanti3/bin:/usr/local/bin:/usr/bin:/bin worked for me, but I'll swap it to conda run -n sqanti3

Thanks

[Fabian-RY]

Improving the compatibility with nextflow would be a nice touch. I'll look into it, to give an official way to execute sqanti3 in a nextflow pipeline to avoid cases like this one. In the meantime, I'll update the FAQ and wiki to reflect the information you gave us for the people that, like you, try to introduce it into a nextflow pipeline.