{"type":"doc","content":[{"type":"paragraph","content":[{"text":"Goal","type":"text","marks":[{"type":"strong"}]},{"text":": Introduce how conda environments can be reproduced and shared.","type":"text"}]},{"type":"paragraph","content":[{"text":"Based on ","type":"text"},{"text":"Managing Environments","type":"text","marks":[{"type":"link","attrs":{"href":"https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html"}}]},{"text":".","type":"text"}]},{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"style":{"value":"none"}},"macroMetadata":{"macroId":{"value":"2cee5b56-9357-429f-8feb-ba69f70aaf14"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"c253b8de-ffd4-42ca-a941-cbf3116bc513"}},{"type":"rule"},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"In the following examples, we assume you already have a ","type":"text"},{"text":"miniconda3","type":"text","marks":[{"type":"code"}]},{"text":" module already loaded.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Clone an Environment","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Existing Conda environments can be cloned (essentially copied).","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ conda create --help\n...\noptions:\n...\n --clone ENV Create a new environment as a copy of an existing local environment.\n...","type":"text"}]},{"type":"paragraph","content":[{"text":"Example","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[]$ conda create -p py_env2 --clone py_env\nRetrieving notices: ...working... done\nSource: /home//.conda/envs/py_env\nDestination: /cluster/medbow/project///software/py_env2\nPackages: 39\nFiles: 1\n...\n#\n# To activate this environment, use\n# $ conda activate /cluster/medbow/project///software/py_env2","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Notice","type":"text","marks":[{"type":"strong"}]},{"text":": The ","type":"text"},{"text":"source","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" (environment being cloned) and the ","type":"text"},{"text":"destination","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" (new cloned environment) are listed.","type":"text"}]},{"type":"paragraph","content":[{"text":"In the above, we are using the ","type":"text"},{"text":"-p","type":"text","marks":[{"type":"code"}]},{"text":" option so the destination is within the current working directory, and cloning from an existing environment that was created within the default environment location - so only its name (not absolute path) is required.","type":"text"}]}]},{"type":"expand","attrs":{"title":"Full Details:"},"content":[{"type":"codeBlock","content":[{"text":"[]$ pwd\n/project///software\n[]$ ls\nslim_env_4.2.2\n\n[]$ conda create -p py_env2 --clone py_env\nRetrieving notices: ...working... done\nSource: /home//.conda/envs/py_env\nDestination: /cluster/medbow/project///software/py_env2\nPackages: 39\nFiles: 1\n\nDownloading and Extracting Packages:\n\n\nDownloading and Extracting Packages:\n\nPreparing transaction: done\nVerifying transaction: done\nExecuting transaction: done\n#\n# To activate this environment, use\n#\n# $ conda activate /cluster/medbow/project///software/py_env2\n#\n# To deactivate an active environment, use\n#\n# $ conda deactivate\n\n\n[]$ ls\npy_env2 slim_env_4.2.2","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Using Cloned Environment","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Notice how you need to activate/use this cloned environment:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ cat ~/.conda/environments.txt\n/home//.conda/envs/py_env\n/project///conda/envs/r_env\n/cluster/medbow/project///software/slim_env_4.2.2\n/cluster/medbow/project///software/py_env2\n\n\n[]$ conda info --env\n# conda environments:\n#\nbase /apps/u/opt/linux/miniconda3/24.3.0\n /cluster/medbow/project///software/py_env2\n /cluster/medbow/project///software/slim_env_4.2.2\npy_env /home//.conda/envs/py_env\nr_env /project///conda/envs/r_env","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Need to define the full path to ","type":"text"},{"text":"activate","type":"text","marks":[{"type":"em"}]},{"text":".","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ conda activate /cluster/medbow/project///software/py_env2\n(/cluster/medbow/project///software/py_env2) []$ ","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Conda env command","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"env","type":"text","marks":[{"type":"code"}]},{"text":" sub-command provides the a process that can be used to ","type":"text"},{"text":"export","type":"text","marks":[{"type":"code"}]},{"text":" into a ","type":"text"},{"text":"readable text file","type":"text","marks":[{"type":"em"}]},{"text":" a description of the entire Conda environment that can then used to ","type":"text"},{"text":"create","type":"text","marks":[{"type":"code"}]},{"text":" (essentially import) to replicate.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ conda env --help\nusage: conda env [-h] command ...\n\npositional arguments:\n command\n config Configure a conda environment.\n create Create an environment based on an environment definition file.\n export Export a given environment\n list List the Conda environments.\n remove Remove an environment.\n update Update the current environment based on environment file.\n\noptions:\n -h, --help Show this help message and exit.","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Export an Environment","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Within an active environment we can export into a readable file a description of the entire Conda environment. This describes all the ","type":"text"},{"text":"system","type":"text","marks":[{"type":"em"}]},{"text":" related libraries as well as anything that that was explicitly ","type":"text"},{"text":"conda install","type":"text","marks":[{"type":"code"}]},{"text":"-ed.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ conda activate r_env\n(r_env) []$ conda env export > r_env.yml\n(r_env) []$ conda deactivate\n\n[]$ cat r_env.yml\nname: r_env\nchannels:\n - conda-forge\n - defaults\ndependencies:\n - _libgcc_mutex=0.1=main\n...\n - zstd=1.5.5=hc292b87_2\nprefix: /project///conda/envs/r_env","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Import an Environment","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":" Using the ","type":"text"},{"text":"env create","type":"text","marks":[{"type":"code"}]},{"text":" sub-command we can then define a file to read/import that describes the environment we want to create - essentially cloning it.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ cd /project///software/\n[]$ conda env create -p r_env2 --file r_env.yml\n...\n#\n# To activate this environment, use\n#\n# $ conda activate /cluster/medbow/project///software/r_env2\n...","type":"text"}]},{"type":"rule"},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"1eaad22f-492c-423c-8932-d253b8b44203"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[333.0]},"content":[{"type":"paragraph","content":[{"text":"Prev","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Example 03: Applications: SLiM","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2175369284"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[326.0]},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"Workshop Home","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"Intro to Using Conda","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2135883799"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[349.0]},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"end"}}],"content":[{"text":"Next","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"end"}}],"content":[{"text":"Example 04: Application: Qiime Ecosystem","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2175402045"}}]}]}]}]}]},{"type":"paragraph","content":[{"text":" ","type":"text"}]}],"version":1}

Browser not supported