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nextflow/docs/install.md

@@ -0,0 +1,177 @@
+(install-page)=
+
+# Installation
+
+Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). This page describes how to install Nextflow.
+
+:::{note}
+New versions of Nextflow are released regularly. See {ref}`updating-nextflow-page` for more information about Nextflow release cadence, how to update Nextflow, and how select your version of Nextflow.
+:::
+
+(install-requirements)=
+
+## Requirements
+
+Nextflow requires Bash 3.2 (or later) and [Java 17 (or later, up to 26)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. To see which version of Java you have, run the following command:
+
+```{code-block} bash
+:class: copyable
+java -version
+```
+
+:::{versionchanged} 24.11.0-edge
+Support for Java versions prior to 17 was dropped.
+:::
+
+If you don't have a compatible version of Java installed, it is recommended that you install it through [SDKMAN!](https://sdkman.io/), and that you use the latest Long-Term-Support (LTS) version of Temurin. See [Which version of JDK should I use?](https://whichjdk.com/) for more information about different versions of Java.
+
+To install Java with SDKMAN:
+
+1. [Install SDKMAN](https://sdkman.io/install):
+
+    ```{code-block} bash
+    :class: copyable
+    curl -s https://get.sdkman.io | bash
+    ```
+
+2. Open a new terminal.
+
+3. Install Java:
+
+    ```{code-block} bash
+    :class: copyable
+    sdk install java 17.0.10-tem
+    ```
+
+4. Confirm that Java is installed correctly:
+
+    ```{code-block} bash
+    :class: copyable
+    java -version
+    ```
+
+(install-nextflow)=
+
+## Install Nextflow
+
+Nextflow is distributed as an easy to use self-installing package. It is also distributed via Conda and as a standalone distribution.
+
+### Self-install
+
+In order to make the installation process as simple as possible, Nextflow is distributed as a self-installing package.
+
+To install Nextflow with the self-installing package:
+
+1. Download Nextflow:
+
+    ```{code-block} bash
+    :class: copyable
+    curl -s https://get.nextflow.io | bash
+    ```
+
+    :::{tip}
+    Set `export CAPSULE_LOG=none` to make the installation logs less verbose.
+    :::
+
+2. Make Nextflow executable:
+
+    ```{code-block} bash
+    :class: copyable
+    chmod +x nextflow
+    ```
+
+3. Move Nextflow into an executable path. For example:
+
+    ```{code-block} bash
+    :class: copyable
+    mkdir -p $HOME/.local/bin/
+    mv nextflow $HOME/.local/bin/
+    ```
+
+    :::{tip}
+    Ensure the directory `$HOME/.local/bin/` is included in your `PATH` variable. Temporarily add this directory to `PATH` by setting `export PATH="$PATH:$HOME/.local/bin"`. Add the directory to `PATH` permanently by adding the export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`. Alternatively, move the `nextflow` executable to a directory already in your `PATH`.
+    :::
+
+    :::{warning}
+    Nextflow updates its executable during the self-install process, therefore the update can fail if the executable is placed in a directory with restricted permissions.
+    :::
+
+4. Confirm Nextflow is installed correctly:
+
+    ```{code-block} bash
+    :class: copyable
+    nextflow info
+    ```
+
+### Conda
+
+To install Nextflow with Conda:
+
+1. Create an environment with Nextflow:
+
+    ```{code-block} bash
+    :class: copyable
+    conda create --name nf-env bioconda::nextflow
+    ```
+
+2. Activate the environment:
+
+    ```{code-block} bash
+    :class: copyable
+    source activate nf-env
+    ```
+
+3. Confirm Nextflow is installed correctly:
+
+    ```{code-block} bash
+    :class: copyable
+    nextflow info
+    ```
+
+:::{warning}
+Installing Nextflow via Conda may lead to outdated versions, dependency conflicts, and Java compatibility issues. Using the self-installing package is recommended for a more reliable and up-to-date installation.
+:::
+
+(install-standalone)=
+
+### Standalone distribution
+
+The Nextflow standalone distribution (i.e., the `dist` release) is a self-contained `nextflow` executable that can run without needing to download core dependencies at runtime. This distribution is useful for offline environments as well as building and testing Nextflow locally.
+
+To use the standalone distribution:
+
+1. Download the standalone distribution from Assets section of the [GitHub releases page](https://github.com/nextflow-io/nextflow/releases).
+
+2. Grant execution permissions to the downloaded file. For example:
+
+    ```{code-block} bash
+    :class: copyable
+    chmod +x nextflow-24.10.1-dist
+    ```
+
+3. Use it as a drop-in replacement for `nextflow` command. For example:
+
+    ```{code-block} bash
+    :class: copyable
+    ./nextflow-24.10.1-dist run info
+    ```
+
+:::{note}
+The standalone distribution will still download core and third-party plugins as needed at runtime.
+:::
+
+## Seqera Platform
+
+You can launch workflows directly from [Seqera Platform](https://seqera.io/platform/) without installing Nextflow locally.
+
+Launching from Seqera provides you with:
+
+- User-friendly launch interfaces.
+- Automated cloud infrastructure creation.
+- Organizational user management.
+- Advanced analytics with resource optimization.
+
+Seqera Cloud Basic is free for small teams. Researchers at qualifying academic institutions can apply for free access to Seqera Cloud Pro.
+See [Seqera Platform Cloud](https://docs.seqera.io/platform) to get started.
+
+If you have installed Nextflow locally, you can use the {ref}`nextflow auth <cli-auth>` command to authenticate with Seqera and automatically configure workflow monitoring.