Potential setup issue

[susheelbhanu]

Hey @Arkadiy-Garber

I was trying to re-setup MagicLamp and noticed the following potential issue. In the setup.sh script which looks like so:

conda create -n fegenie -c r r-ggplot2 r-stringi r-reshape r-reshape2 r-tidyverse r-argparse r-ggdendro r-pvclust python=3.7 hmmer diamond prodigal blast metabat2 --yes

## activating environment
source activate magiccave

Line #11 creates a conda environment called "fegenie". However, lines #18 and 49 are activating an environment called "magiccave"

ERROR

# To activate this environment, use
#
#     $ conda activate fegenie
#
# To deactivate an active environment, use
#
#     $ conda deactivate

setup.sh: line 13: Rscript: command not found
setup.sh: line 14: Rscript: command not found
setup.sh: line 15: Rscript: command not found
setup.sh: line 18: activate: No such file or directory
mkdir: cannot create directory ‘/etc/conda’: Permission denied
setup.sh: line 46: /etc/conda/activate.d/env_vars.sh: No such file or directory
setup.sh: line 49: activate: No such file or directory

        DONE!

Thanks again for a great pipeline!

[Arkadiy-Garber]

Hi Susheel,

Thanks for your interest in MagicLamp! And thanks for letting me know about this issue. I see there is a typo in the setup.sh script. I just fixed this, and re-named the conda environment to 'magiclamp'. If you re-run bash setup.sh, this error should be resolved. Let me know if you have any questions or run into any other issues.

Thanks! Arkadiy

[susheelbhanu]

Thanks @Arkadiy-Garber!