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pirovc / metameta

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Conda environments are only allowed with shell, script or wrapper directives (not with run). - preproc.sm", line 27 #1

Closed spabinger closed 7 years ago

spabinger commented 7 years ago

Hi,

I installed MetaMeta according to the description on the Github page, but when I try to start the program it fails with the following error:

RuleException in line 27 of /home/stephan/work/miniconda/data/opt/metameta/scripts/preproc.sm:
Conda environments are only allowed with shell, script or wrapper directives (not with run).
  File "/home/stephan/work/miniconda/data/opt/metameta/Snakefile", line 24, in <module>
  File "/home/stephan/work/miniconda/data/opt/metameta/scripts/preproc.sm", line 27, in <module>

Do you know how to fix it?

Thanks, Stephan

pirovc commented 7 years ago

Hi @spabinger,

Did you run MetaMeta with the --use-conda parameter? Is Snakemake on version 3.9.1? If you are running it with some queuing system (slurm, torque, etc) you will need to pre-install the tools before running MetaMeta (check README ).

Best, Vitor

spabinger commented 7 years ago

Hi,

thanks for the fast reply.

Best, Stephan

pirovc commented 7 years ago

I believe the problem is the Snakemake version. MetaMeta was developed and tested on version 3.9.1 and this is the only version supported by now. I recommend you to downgrade to 3.9.1 via conda (conda install -c bioconda snakemake=3.9.1).

If you need the recent version for other applications I recommend to install and run MetaMeta on a separated environment:

conda create -c bioconda -n metameta metameta=1.1
source activate metameta
metameta --configfile epitype_test.yaml --use-conda --keep-going --cores 32
source deactivate

Please let me know if that solves the problem. Vitor

spabinger commented 7 years ago

Thanks for your help - it's running right now :-)

Best, Stephan