Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

singularity bind point error in workflow #123

Open
cgrahlm opened this issue Jul 25, 2018 · 0 comments
Open

singularity bind point error in workflow #123

cgrahlm opened this issue Jul 25, 2018 · 0 comments

Comments

@cgrahlm
Copy link

cgrahlm commented Jul 25, 2018

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_
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant