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Community/Logs

Galaxy Community Log Board

The Galaxy Community Log Board is a place to share how you addressed a particular task in your Galaxy deployment. Log entries describe specific solutions to particular tasks, such as the details of what steps were taken to deploy Galaxy on particular platforms, or with particular software. It's an easy way to help others (and learn from others) by sharing what you've already done.

So, if you have figured out how to do something, and it took you a while, then this is the ideal forum for sharing that information with the community.

Logs

2016

2015

Date Topic Resolution Who
2015/12/08 Testing connexion between Galaxy and iRODS Testing the connexion of Galaxy to iRODS object store Mikael Loaec, Olivier Inizan
2015/10/21 Galaxy Tool Generating Datasets How to generate dataset collections from a Galaxy tool Steve Cassidy
2015/10/09 How Galaxy resolves tool dependencies (or not) Explanation of Galaxy's tool dependency definitions that specify how to source the actual packages that implement the tool’s commands. Peter van Heusden
2015/07/30 Moving from MySQL to PostgreSQL. It is pretty simple, though you might hit some obstacles depending on how old your MySQL server is and how much you have manually interfered with the database. Hans-Rudolf Hotz
2015/07/12 BioJS2Galaxy - A step by step guide To encourage the use of BioJavaScript (BioJS) visualisations in Galaxy we decided to create this simple step by step guide on how to use Sebastian Wilzbach’s application, biojs2galaxy. Benedikt Rauscher, Benjamen White
2015/06/02 Exposing Galaxy reports via nginx in a production instance Outline how I've done this for our local Galaxy set up, which uses nginx. Peter Briggs
2015/04/22 Using GALAXY_SLOTS with multithreaded Galaxy tools Using GALAXY_SLOTS with multithreaded Galaxy tools. Peter Briggs
2015/03/18 Installing ANNOVAR in Galaxy A HOWTO for installing ANNOVAR in Galaxy. Peter Briggs
2015/02/28 Integrating a Java Program in Galaxy Example showing how to install a Java program as a tool in a Galaxy instance. Pierre Lindenbaum
2015/02/12 FTP upload to Galaxy using ProFTPd and PBKDF2 ProFTPd implemented using PBKFD2 protocol for encryption Peter Briggs
2015/02/09 Instalando um servidor do Galaxy Project Portuguese Galaxy Documentation Léo Biscassi

2014

Date Topic Resolution Who
2014/09/01 Overview of Galaxy on Bio-Linux 8. Information about running Galaxy under Bio-Linux 8 Tracey Timms-Wilson, NERC Environmental 'Omics Synthesis Centre
2014/06/10 Setting up a secure tool shed with remote authentication requires some tweaks in order to allow Galaxy to communicate with the tool shed. Works and isn't much additional work above setting up Galaxy with SSL and LDAP. William Holtz
2014/03/20 Basic Galaxy Puppet Module A puppet module for a very basic galaxy server (use for development) Olivier Inizan, Mikael Loaec
2014/01/27 Problem with logout when using LDAP for authentication with remoteUser enabled. Make changes to 4 Galaxy configuration files Tim Booth

2013

Add a Log Entry

Have experience you want to share?  The larger Galaxy community would love to learn about it.  There are two ways to add your deployment to this catalog.

  1. Use the Wiki

    • Log entry is added to the board immediately, but requires a wiki account
  2. Use the Online Form

    • Some delay in publishing log entries, and less control over what it looks like, but interface is much easier.

Use the Wiki

  1. Login to the wiki. If you don't have an account, you'll need to create one.

  2. Pick a good descriptive, CamelCase name for your log file.  This will become part of the URL for your log page.  This can include descriptive text, a date (but not the year as that is automatically included), your name or anything else that helps identify the log.  Avoid embedded spaces as they make lousy URLs.

  3. Type the CamelCase name in box below and hit the "Create" button.

  4. A template for the new log page will appear.  Replace the template text with details about your experience
  5. Save, review, and edit the page until you are happy with it.
  6. Return to this page, edit this page, and add a link to your log page, and then save the edit.

Use the Online Form

If the wiki option seems a little daunting, you can also create an entry that just links to an external document that uses whatever documentation technology you are most comfortable with. Use this form to create and entry that just points to the real documentation. Once the form has been submitted, the information will be reviewed and a log entry will be programmatically generated within a week or two. You will be notified via email when the entry is created.

   Submit a log entry using the online form