82 lines
3.1 KiB
Markdown
82 lines
3.1 KiB
Markdown
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[](https://snakemake.readthedocs.io)
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[](https://www.rapids.science/)
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[](code_of_conduct.md)
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# RAPIDS
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**R**eproducible **A**nalysis **Pi**peline for **D**ata **S**treams
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For more information refer to our [documentation](http://www.rapids.science)
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By [MoSHI](https://www.moshi.pitt.edu/), [University of Pittsburgh](https://www.pitt.edu/)
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## Installation
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For RAPIDS installation refer to to the [documentation](https://www.rapids.science/1.8/setup/installation/)
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## For the installation of the Docker version
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1. Follow the [instructions](https://www.rapids.science/1.8/setup/installation/) to setup RAPIDS via Docker (from scratch).
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2. Delete current contents in /rapids/ folder when in a container session.
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```
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cd ..
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rm -rf rapids/{*,.*}
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cd rapids
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```
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3. Clone RAPIDS workspace from Git and checkout a specific branch.
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```
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git clone "https://repo.ijs.si/junoslukan/rapids.git" .
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git checkout <branch_name>
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```
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4. Install missing “libpq-dev” dependency with bash.
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```
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apt-get update -y
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apt-get install -y libpq-dev
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```
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5. Restore R venv.
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Type R to go to the interactive R session and then:
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```
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renv::restore()
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```
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6. Install cr-features module
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From: https://repo.ijs.si/matjazbostic/calculatingfeatures.git -> branch modifications_for_rapids.
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Then follow the "cr-features module" section below.
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7. Install all required packages from environment.yml, prune also deletes conda packages not present in environment file.
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```
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conda env update --file environment.yml –prune
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```
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8. If you wish to update your R or Python venvs.
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```
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R in interactive session:
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renv::snapshot()
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Python:
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conda env export --no-builds | sed 's/^.*libgfortran.*$/ - libgfortran/' | sed 's/^.*mkl=.*$/ - mkl/' > environment.yml
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```
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## cr-features module
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This RAPIDS extension uses cr-features library accessible [here](https://repo.ijs.si/matjazbostic/calculatingfeatures).
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To use cr-features library:
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- For now, use the "modifications_for_rapids" branch to get the newest version of cr-features that is functional for RAPIDS-STRAW analysis.
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- Follow the installation instructions in the [README.md](https://repo.ijs.si/matjazbostic/calculatingfeatures/-/blob/master/README.md).
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- Copy built calculatingfeatures folder into the RAPIDS workspace.
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- Install the cr-features package by:
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```
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pip install path/to/the/calculatingfeatures/folder
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e.g. pip install ./calculatingfeatures if the folder is copied to main parent directory
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cr-features package has to be built and installed everytime to get the newest version.
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Or an the newest version of the docker image must be used.
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``` |