{"type":"doc","content":[{"type":"paragraph","content":[{"text":"Goal","type":"text","marks":[{"type":"strong"}]},{"text":": Demonstrate importing the large ","type":"text"},{"text":"qiime","type":"text","marks":[{"type":"link","attrs":{"href":"https://qiime2.org/"}}]},{"text":" application ecosystem.","type":"text"}]},{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"style":{"value":"none"}},"macroMetadata":{"macroId":{"value":"e0fe8b48-131a-4825-8e81-f72509880fd9"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"f095f9ef-e5c3-4715-bd1e-86974fc21c34"}},{"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":"Can I use a Channel","type":"text"}]},{"type":"paragraph","content":[{"text":"Not from the channels I have configured.","type":"text"}]},{"type":"codeBlock","content":[{"text":"[]$ conda search qiime\nLoading channels: done\nNo match found for: qiime. Search: *qiime*\n# Name Version Build Channel\nr-qiimer 0.9.4 r3.3.2_0 conda-forge\n...\nr-qiimer 0.9.4 r43hc72bb7e_1005 conda-forge","type":"text"}]},{"type":"paragraph","content":[{"text":"Only older versions in bioconda channel.","type":"text"}]},{"type":"codeBlock","content":[{"text":"[]$ conda search bioconda::qiime\nLoading channels: done\n# Name Version Build Channel\nqiime 1.8.0 py27_0 bioconda\n...\nqiime 1.9.1 py_3 bioconda","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Using a Definition File","type":"text"}]},{"type":"paragraph","content":[{"text":"From Install QIIME2 within a conda environment","type":"text","marks":[{"type":"link","attrs":{"href":"https://docs.qiime2.org/2024.5/install/native/#install-qiime-2-within-a-conda-environment"}}]},{"text":":","type":"text"}]},{"type":"codeBlock","content":[{"text":"[]$ pwd\n/project///software\n[]$ mkdir qiime\n[]$ cd qiime/\n[]$ wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-linux-conda.yml\n\n[]$ conda env create -p amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml\n\n[]$ conda activate /cluster/medbow/project///software/qiime/amplicon-2024.5\n(/cluster/medbow/project///software/qiime/amplicon-2024.5) []$ qiime info\nSystem versions\nPython version: 3.9.19\nQIIME 2 release: 2024.5\nQIIME 2 version: 2024.5.0\nq2cli version: 2024.5.0\n...","type":"text"}]},{"type":"mediaGroup","content":[{"type":"media","attrs":{"id":"841a204f-6e76-401f-ae64-b2b8d785d618","collection":"contentId-2175402045","type":"file"}}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"What’s in this Qiime Environment?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"This environment contains qiime commands, R and libraries, Python and packages…","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"(/cluster/medbow/project///software/qiime/amplicon-2024.5) []$ which R\n/cluster/medbow/project///software/qiime/amplicon-2024.5/bin/R\n(/cluster/medbow/project///software/qiime/amplicon-2024.5) []$ R --version\nR version 4.3.3 (2024-02-29) -- \"Angel Food Cake\"\n\n(/cluster/medbow/project///software/qiime/amplicon-2024.5) []$ which python\n/cluster/medbow/project///software/qiime/amplicon-2024.5/bin/python\n(/cluster/medbow/project///software/qiime/amplicon-2024.5) []$ python --version\nPython 3.9.19\n\n(/cluster/medbow/project///software/qiime/amplicon-2024.5) []$ pip list -v\nPackage Version Location Installer\n------------------------- -------------- ------------------------------------------------------------------------------------------------ ---------\naltair 5.3.0 /cluster/medbow/project///software/qiime/amplicon-2024.5/lib/python3.9/site-packages conda\nanyio 4.3.0 /cluster/medbow/project///software/qiime/amplicon-2024.5/lib/python3.9/site-packages conda\n...","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"How Large is this Environment?","type":"text"}]},{"type":"codeBlock","content":[{"text":"[qiime]$ du -d 1 -h\n4.6G ./amplicon-2024.5\n4.6G .","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"This is just the qiime environment. It does not include all the packages that were downloaded.","type":"text"}]},{"type":"paragraph","content":[{"text":"What about all the other environments we have created?","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[software]$ du -d 1 -h\n1.2G ./py_env2\n4.6G ./qiime\n1.1G ./r_env2\n11M ./slim_env_4.2.2\n6.8G .\n\n[conda]$ du -d 1 -h\n1.2G ./envs\n8.3G ./pkgs\n9.5G .","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"With just a few environments we are using >15G of storage - do you want this within your home folder?","type":"text"}]},{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":".pkgs","type":"text","marks":[{"type":"code"}]},{"text":" folder can be cleaned up, and packages will just be downloaded again if needed.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Cleaning Up","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Conda provides the ","type":"text"},{"text":"clean","type":"text","marks":[{"type":"link","attrs":{"href":"https://docs.conda.io/projects/conda/en/latest/commands/clean.html"}}]},{"text":" command: Remove unused packages and caches.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ module load miniconda3/24.3.0\n[]$ conda clean -a\nWill remove 947 (2.00 GB) tarball(s).\nWill remove 1 index cache(s).\nWill remove 32 (10.0 MB) package(s).\nThere are no tempfile(s) to remove.\nThere are no logfile(s) to remove.\n[]$","type":"text"}]},{"type":"codeBlock","content":[{"text":"[conda]$ du -d 1 -h\n0 ./.empty\n1.2G ./envs\n6.0G ./pkgs","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"We managed to clean up 2.3G of packages.","type":"text"}]}]},{"type":"rule"},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"69fc13e7-c702-4664-99c7-b3fc0df0bfe3"},"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":"Reproducibility and Sharing","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2175631444"}}]}]}]},{"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":"Conda with salloc and sbatch","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2236645429"}}]}]}]}]}]},{"type":"paragraph"},{"type":"paragraph"},{"type":"paragraph"}],"version":1}

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