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dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
https://dahak-metagenomics.github.io/dahak
BSD 3-Clause "New" or "Revised" License
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singularity bind point error in workflow #123

Open cgrahlm opened 6 years ago

cgrahlm commented 6 years ago

Expected behavior

Running workflow from The Really Quick Copy-And-Paste Quick Start should run the singularity fastqc container.

Actual behavior

Gets: WARNING: Non existent bind point (file) in container: '/etc/localtime' WARNING: Skipping user bind, non existent bind point (directory) in container: '/data Then errors out with: Specified output directory '/data' does not exist

Steps to reproduce the behavior

Gets error on both Ubuntu 18.04 and Centos 6.10.

export SINGULARITY_BINDPATH="data:/data"
snakemake --use-singularity -p --configfile=config/custom_readfilt_workflow.json read_filtering_pretrim_workflow

Some issue with the singularity binding? Tried running with the following:

(dahak) [cgrahlmann@localhost workflows]$ singularity exec --home /home/cgrahlmann/mondavi/dahak/workflows  /home/cgrahlmann/mondavi/dahak/workflows/.snakemake/singularity/f1d03c0a142609dc68fd5a6943abcaad.simg bash -c 'ls'
WARNING: Non existent bind point (file) in container: '/etc/localtime'
WARNING: Skipping user bind, non existent bind point (directory) in container: '/data'
GettingStarted.md         WorkflowComponents.md     comparison                dataset_construction      run_assembly.sh           run_taxclass.sh           test_assembly.sh          test_taxclass.sh
README.md                 Workflows.md              config                    functional_inference      run_comparison.sh         run_workflows.sh          test_comparison.sh
Snakefile                 assembly                  data                      read_filtering            run_readfiltering.sh      taxonomic_classification  test_readfilt.sh_