diff --git a/docs/tutorial_0_install.md b/docs/tutorial_0_install.md index eac09eaf..d2b650fe 100644 --- a/docs/tutorial_0_install.md +++ b/docs/tutorial_0_install.md @@ -95,12 +95,58 @@ Now that you have setup the software necessary to start using V-pipe, you can fo For advanced users: If your are fluent with these tools, you can: -* directly download and install [bioconda](https://bioconda.github.io/user/install.html) and [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#installation-via-conda), +* directly download and install [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) (*and perform one-time setup of [bioconda](https://bioconda.github.io/index.html)*) and [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#installation-via-conda), * specifiy your V-pipe configuration, and start using V-pipe Use `--use-conda` to [automatically download and install](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management) any further pipeline dependencies. Please refer to the documentation for additional instructions. -### Reusing an existing conda installation +## Reusing an existing conda installation -[TO BE CONTINUED] +Find out the directory where Conda is currently installed on your system. Common locations include: + +```bash + /opt/conda + ~/miniconda + ~/anaconda + ``` + +Ensure that your `PATH` environment variable includes the path to your existing Conda installation. + +You can do this by editing your shell's configuration file (e.g., `.bashrc`, `.bash_profile`, `.zshrc`). + +Add the `PATH` to the configuration file by adding this line but replace `/path/to/your/conda` with the actual path to your Conda installation directory : + +```bash +export PATH="/path/to/your/conda/bin:$PATH" +``` + +Restart your terminal session to apply the changes made to the environment variables, or run: + +```bash +source ~/.bashrc +``` + +This command reloads the shell configuration file (replace `.bashrc` with the appropriate file if you're using a different shell). + +Download the V-pipe installation script using `curl`: + +```bash +curl -O 'https://raw.githubusercontent.com/cbg-ethz/V-pipe/master/utils/quick_install.sh' +``` + +Make the script executable if it doesn't have permissions: + +```bash +chmod +x quick_install.sh +``` + +Run the installation script with the desired parameters to specify the installation directory (`-p`) and working directory (`-w`). For example: + +```bash +bash quick_install.sh -p vp-analysis -w work +``` + +Here, `-p vp-analysis` specifies the subdirectory where V-pipe will be installed, and `-w work` creates a working directory for V-pipe. + +After the installation completes, verify that V-pipe and its dependencies are correctly installed by running commands like `conda list` to see the installed packages and `vpipe --help` to check if V-pipe commands are available. \ No newline at end of file