Snakemake test not working!

susheelbhanu commented 5 years ago

Hi,

I've installed the conda version, and when running the test am getting the following:

WorkflowError: Failed to open /mnt/irisgpfs/projects/ecosystem_biology/local_tools/MAGpy/MAGpy.

I've checked folder permissions and everything looks alright.

Could you let me know how to fix this?

Thank you, Susheel

yshengzhi commented 4 years ago

Hi, I have a same problem. Have you solved it yet?

susheelbhanu commented 4 years ago

Nope, not yet.

mw55309 commented 4 years ago

Hi everyone

Make sure you are inside the MAGpy directory after cloning:

cd MAGpy

snakemake --use-conda -s MAGpy test

Does that help?

susheelbhanu commented 4 years ago

Thanks a lot Mick, that seems to be the trick! A successful dry-run

snakemake --use-conda -s MAGpy test --cores 4 -np
Building DAG of jobs...
Error: Directory cannot be locked. This usually means that another Snakemake instance is running on this directory. Another possibility is that a previous run exited unexpectedly.
Conda environment envs/prodigal.yaml will be created.
Conda environment envs/basic2.yaml will be created.
Conda environment envs/diamond.yaml will be created.
Conda environment envs/sourmash.yaml will be created.
Conda environment envs/bioperl.yaml will be created.
Conda environment envs/checkm.yaml will be created.
Conda environment envs/ete3.yaml will be created.
Job counts:
        count   jobs
        1       test
        1       test_checkm
        1       test_checkm_plus
        1       test_diamond
        1       test_diamond_bin_summary_plus
        1       test_diamond_report
        1       test_phylophlan
        1       test_prodigal
        1       test_sourmash
        9

WatsonLab / MAGpy

Snakemake test not working! #15