Hi,

During the Hackathon, I wanted to test the bioconda dependencies and while initializing planemo to get conda working, I got this:

Remis-MacBook-Pro:vegan remi$ planemo conda_init wget -q --recursive -O- 'https://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh' >> '/var/folders/2v/kplq53zj2c3frn0fq5hsp0wc0000gn/T/conda_insta llkWrXlu.bash'; bash '/var/folders/2v/kplq53zj2c3frn0fq5hsp0wc0000gn/T/conda_installkWrXlu.bash' -b -p '/Users/remi/miniconda2' -k or -r can be used together with -O only if outputting to a regular file.

And then the tests are failing because it did not find the dependencies (r-vegan: https://github.com/bioconda/bioconda-recipes/tree/ac328e0c63071d3e27cf9f073c380726f1065805/recipes/r-vegan/2.3_4) :

galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-vegan', ignoring galaxy.jobs.command_factory: INFO: Built script [/var/folders/2v/kplq53zj2c3frn0fq5hsp0wc0000gn/T/tmpyoAm_5/job_working_directory/000/2/tool_script.sh] for tool command[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan' > /var/folders/2v/kplq53zj2c3frn0fq5hsp0wc0000gn/T/tmpyoAm_5/tmp/GALAXY_VERSION_STR ING_2 2>&1; Rscript "/var/folders/2v/kplq53zj2c3frn0fq5hsp0wc0000gn/T/tmpyoAm_5/job_working_directory/000/2/tmpeQL4tC"]

Thanks!