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rnajena / poseidon

PoSeiDon: positive selection detection and recombination analysis pipeline
MIT License
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Profile selection in conda environment #26

Open burcudsr opened 3 years ago

burcudsr commented 3 years ago

Dear Poseidon team,

I have a question about -profile selection. I am trying to run example file called "bats_mx1_small.fasta" on a HPC using Singularity but also running nextflow via miniconda environment.

When i set -profile slurm,conda give me an error like:

Unknown configuration profile: 'conda' Did you mean one of these? yoda

When i set -profile slurm,singularity give me an error like:

Error executing process > 'check_fasta_format (1)' Caused by: Failed to submit process to grid scheduler for execution Command executed: sbatch .command.run Command exit status: 1 Command output: sbatch: error: Batch job submission failed: Unspecified error

Do you have any suggestions about that, i am new to nextflow. I will be glad for your contributions.

hoelzer commented 3 years ago

Dear @burcudsr , thanks for using PoSeiDon!

Unfortunately, there is currently no conda env available. The pipeline is tested with Docker support which might be only available on your HPC via Singularity. However, I did not fully test the pipeline under singularity yet.

You can give it a try via -profile slurm,singularity

I hope that works, otherwise please just let me know!

burcudsr commented 3 years ago

Dear @hoelzer , thanks for your quick reply.

I tried with -profile slurm,singularity on HPC and can't find singularity command which is in /usr/bin/singularity . However, I managed to run test_file -profile local,docker without any errors on my local computer, so I'll try to run my files from there.

hoelzer commented 3 years ago

Hi,

on your HPC you maybe have to load singularity as a module:

module load singularity

is 

singularity --version

working?

Otherwise, when your data is not to large it should also run w/ Docker on a laptop (just might need some more time)