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Installation Doc Update #153

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52 changes: 49 additions & 3 deletions docs/tutorial_0_install.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.