Difference between revisions of "Conda"
(Created page with "WIP for progressing to user-centric conda installs Dear Cosmika, We are testing Bioconda on Marvin on a per user basis, so you have total control over it. Would you please...") |
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| + | We are testing Bioconda on Marvin on a per user basis, so you have total control over it. | ||
Log in and from the command line type: | Log in and from the command line type: | ||
| − | install-bioconda | + | install-bioconda |
Either log out and back in or type: | Either log out and back in or type: | ||
| − | source ~/.bashrc | + | source ~/.bashrc |
We strongly advise using environments: https://conda.io/docs/user-guide/tasks/manage-environments.html . You can do this in many ways. Please see the link for more details (here you can specifiy eact version etc ..). The easiest usage would be: e.g. conda create -n NAME_OF_ENV PACKAGE_TO_INSTALL | We strongly advise using environments: https://conda.io/docs/user-guide/tasks/manage-environments.html . You can do this in many ways. Please see the link for more details (here you can specifiy eact version etc ..). The easiest usage would be: e.g. conda create -n NAME_OF_ENV PACKAGE_TO_INSTALL | ||
| − | conda create -n roary roary | + | conda create -n roary roary |
| − | conda activate roary | + | conda activate roary |
| − | conda update roary | + | conda update roary |
You are now ready to use this package. | You are now ready to use this package. | ||
| − | Conda deactivate to leave this environment. | + | Conda deactivate to leave this environment. |
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To list all the environments you have created: | To list all the environments you have created: | ||
| − | conda info –envs | + | conda info –envs |
installing packages: https://bioconda.github.io/recipes.html | installing packages: https://bioconda.github.io/recipes.html | ||
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Revision as of 14:41, 23 October 2018
WIP for progressing to user-centric conda installs
We are testing Bioconda on Marvin on a per user basis, so you have total control over it. Log in and from the command line type:
install-bioconda
Either log out and back in or type:
source ~/.bashrc
We strongly advise using environments: https://conda.io/docs/user-guide/tasks/manage-environments.html . You can do this in many ways. Please see the link for more details (here you can specifiy eact version etc ..). The easiest usage would be: e.g. conda create -n NAME_OF_ENV PACKAGE_TO_INSTALL
conda create -n roary roary conda activate roary conda update roary
You are now ready to use this package.
Conda deactivate to leave this environment.
This works for me and a test user. But may fail for you, so be patient with us.
To list all the environments you have created:
conda info –envs
installing packages: https://bioconda.github.io/recipes.html
