Change pip3 to pipx (#2003)

* Change pip3 to pipx

* pipx is not a drop-in replacement for pip

* pipx does not list the injected dependencies

* pipx can run pip list
testing on ubuntu22.04 and 24.04

* Add comment

src/app/loginComponents/onboarding/downloadcliclient/downloadcliclient.component.ts

@@ -86,7 +86,7 @@ run scripts or interact programmatically against Dockstore APIs, and [run workfl
 #### Requirements
 1. Linux/Ubuntu (Recommended - Tested on 22.04 LTS) or Mac OS X machine
 2. Java 17 (Tested with OpenJDK 17 and Eclipse Temurin JDK 17; Oracle JDK may work but is untested)
-3. Python3 and pip3 (Required if working with CWL, optional otherwise)
+3. Python3 and pipx (Required if working with CWL, optional otherwise)
     `;
 
     this.textDataUbuntuLinux = `
@@ -168,23 +168,28 @@ At this point, you now have the Dockstore CLI set up for interacting with the Do
 
 #### Part 6 - Install cwltool (Optional)
 Dockstore relies on [cwltool](https://github.com/common-workflow-language/cwltool) - a reference implementation of CWL - for local execution of tools and workflows described with CWL.
-You'll need to have Python 3 and [pip3](https://pip.pypa.io/en/latest/installing/) to be installed on your machine.
+You'll need to have Python 3 and [pipx](https://pipx.pypa.io/latest/installation/) to be installed on your machine.
 
 **Note:** cwltool must be available on your PATH for the Dockstore CLI to find it.
 
 You can install the version of cwltool that we've tested for use with Dockstore using the following commands:
 1. Install cwltool
 \`\`\`
 curl -o requirements.txt "${this.dsServerURI}/metadata/runner_dependencies?client_version=${this.dockstoreVersion}&python_version=3"
-pip3 install -r requirements.txt
+pipx install cwltool==${this.cwltoolVersion}
+pipx runpip cwltool install -r requirements.txt # this ensures that your version of cwltool and its dependencies matches what we test with
 \`\`\`
-2. Verify using \`pip3 list\` that the installed pip packages match the ones specified in the downloaded requirements.txt. Confirm cwltool installation by checking the version.
+
+**Note:** If you receive a warning saying \`'/YOUR_HOME_DIR/.local/bin' is not on your PATH environment variable.\`, use \`pipx ensurepath\` to add it to your shell's config. Then open a new shell or run \`source ~/.bashrc\`.
+
+2. Verify using that the installed python packages match the ones specified in the downloaded requirements.txt. Confirm cwltool installation by checking the version.
 \`\`\`
+$ pipx runpip cwltool list
 $ cwltool --version
 /usr/local/bin/cwltool ${this.cwltoolVersion}
 \`\`\`
 
-Although Dockstore has only been tested with the above cwltool version, if you have issues installing cwltool please try running \`pip3 install cwltool\`. This will install the latest released version from PyPi that is compatible with your Python version.
+Although Dockstore has only been tested with the above cwltool version, if you have issues installing cwltool please try running \`pipx install cwltool\`. This will install the latest released version from PyPi that is compatible with your Python version.
 
 #### Part 7 - Install Nextflow (Optional)
 The Dockstore CLI does not run Nextflow workflows. Users can run them directly by using the Nextflow command line tool. For installation instructions, follow [Nextflow's documentation](https://github.com/nextflow-io/nextflow#download-the-package)