### Start Galaxy Server with Shell Script

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/events/gcc2014/training-day/admin-walkthrough/index.md

These shell commands initialize and start a Galaxy server instance. The process runs the startup script which configures datatypes and starts the web server on localhost port 8080. The example shows server initialization messages and proper shutdown with Ctrl+C. This completes first-run setup for the Galaxy application.

```console
gxprod@gcc2014:~/galaxy-dist$ sh run.sh
Initializing datatypes_conf.xml from datatypes_conf.xml.sample
  ...
serving on http://127.0.0.1:8080
^C
  ...
gxprod@gcc2014:~/galaxy-dist$ logout
galaxy@gcc2014:~$
```

--------------------------------

### Start Galaxy Instance

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/authnz/cloud/demo/index.md

Starts the local Galaxy instance for the demo. Waits for the server to be ready and serving on http://127.0.0.1:8080. Part of the cloud authorization demo setup.

```bash
./run.sh
```

--------------------------------

### Start Galaxy Server (Bash)

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/events/gcc2014/training-day/admin-walkthrough/index.md

Starts the Galaxy server using the `run.sh` script. This command includes optional caching of dependencies to improve the deployment speed. The server will be accessible at http://127.0.0.1:8080.

```bash
galaxy@gcc2014:~/galaxy-dist$ cp -r ../galaxy-central/eggs eggs  # cache dependencies to speed up deploy (optional)
galaxy@gcc2014:~/galaxy-dist$ sh run.sh
Initializing datatypes_conf.xml from datatypes_conf.xml.sample
  ...
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.3-py2.7.egg
  ...
Fetch successful.
python path is: /home/ubuntu/galaxy-dist/eggs/mercurial-2...
  ...
Starting server in PID 3091.
serving on http://127.0.0.1:8080
```

--------------------------------

### Start Galaxy for the First Time

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/events/gcc2012/training-day/ws5/index.md

Initiates the first-time startup of the Galaxy application using the provided shell script. This process executes initial setup tasks and makes Galaxy accessible via a web interface.

```console
postgres@trainingday:~$ exit
logout
root@trainingday:~# su - galaxy
galaxy@trainingday:~$ cd galaxy-dist
galaxy@trainingday:~/galaxy-dist$ sh run.sh --reload
  ... a lot of output ...
serving on http://127.0.0.1:8080
^C caught in monitor process

galaxy@trainingday:~/galaxy-dist$ 

```

--------------------------------

### Example shed_tool_conf.xml Configuration

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/toolshed/installing-repositories-to-galaxy/index.md

This XML snippet shows the configuration of the shed_tool_conf.xml file after a tool has been installed. It includes details about the tool's location, its unique identifier (guid), and its metadata such as repository name, owner, and version.

```xml
<?xml version="1.0"?>
<toolbox tool_path="../shed_tools">
    <section name="Filter and Sort" id="filter">
        <tool file="localhost/repos/greg/filter/10456b4659aa/filter/filtering.xml" guid="localhost:9009/repos/greg/filter/Filter1/1.0.1">
            <tool_shed>localhost:9009</tool_shed>
            <repository_name>filter</repository_name>
            <repository_owner>greg</repository_owner>
            <changeset_revision>10456b4659aa</changeset_revision>
            <id>Filter1</id>
            <version>1.0.1</version>
        </tool>
    </section>
</toolbox>
```

--------------------------------

### Start Galaxy Server using Bash

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/events/bio-it-world2014/w14/index.md

This bash script initializes and runs the Galaxy server for first-run setup, outputting configuration and server status to console. It depends on Galaxy being properly installed and configured prior to execution, with no input required beyond running the script. The server starts on localhost port 8080 by default, but can be interrupted with Ctrl+C.

```bash
galaxy@bioit:~/galaxy-dist$ sh run.sh
Initializing datatypes_conf.xml from datatypes_conf.xml.sample
  ...
serving on http://127.0.0.1:8080
^C
  ...
galaxy@bioit:~/galaxy-dist$ logout
ubuntu@bioit:~$
```

--------------------------------

### Start Galaxy in Daemon Mode in Bash

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/events/gmod-summer-school2014/index.md

This Bash script runs Galaxy in the background as a daemon, logging to files. Requires sh and Galaxy setup. Input is the --daemon flag; output creates paster.log and paster.pid. Limitation: Cannot be combined with --reload and ignores Ctrl+C.

```bash
$ sh run.sh --daemon
Entering daemon mode
# (No log file this time)
```

--------------------------------

### Install uWSGI and Supervisor (Debian/Ubuntu)

Source: https://github.com/galaxyproject/galaxy-hub/blob/master/content/events/gcc2014/training-day/admin-walkthrough/index.md

Installs the uWSGI application server and the Supervisor process control system on Debian/Ubuntu systems using apt-get. It also removes existing uWSGI startup links.

```console
galaxy@gcc2014:~/galaxy-dist$ sudo apt-get install uwsgi uwsgi-plugin-python supervisor
  ...
After this operation, 4,497 kB of additional disk space will be used.
Do you want to continue? [Y/n]
  ...
galaxy@gcc2014:~/galaxy-dist$ sudo update-rc.d -f uwsgi remove
 Removing any system startup links for /etc/init.d/uwsgi ...
   /etc/rc0.d/K20uwsgi
   /etc/rc1.d/K20uwsgi
   /etc/rc2.d/S20uwsgi
   /etc/rc3.d/S20uwsgi
   /etc/rc4.d/S20uwsgi
   /etc/rc5.d/S20uwsgi
   /etc/rc6.d/K20uwsgi
galaxy@gcc2014:~/galaxy-dist$
```