GENtle/Setup

About - FAQ - Setup - DNA - Protein - PCR and Primer Design - Sequencing - Alignments - Calculators - Virtual Gel - Image Viewer - Tools and Dialogs - Web interface - Graphs and plots - DNA map - Sequence map - Dot plot - Restriction Identifier

Installation

On Windows, run the file GENtleSetup.exe. It will set up GENtle in a directory of your choice, and also prepare for a clean deinstallation.

Databases

There are two types of databases supported by GENtle: File-based (sqlite) and MySQL. By default, a file-based database local.db is set up in the installation directory of GENtle. You can (and should, if access limitations prevent you from working with local.db) create new databases and share them with other users of GENtle in your work group (if you want to).

Database management can be found through the menu "Tools/Manage database", under the tab "Databases".

A quirk:

1. Be careful of using the local db for any real development. I strongly advise that you never put anything into local. That db is in the Gentle program's directory and if, say, you need to reinstall GENtle, or you get a new laptop, you may clobber it. And if someone else takes over after that, you can lose it also. I have seen other strange behavior where local.db gets lost, but can't tie it down for a bug report.

2. GENtle copies blank.db and local.db in [your-username]/AppData/Local/VirtualStore/Program Files (x86)/GENtle It then maintains them. The live local.db is the one in AppData/Local/VirtualStore/Program Files (x86)/GENtle. So, you can delete the one in C:/Program Files (x86)/GENtle and you won't lose it. (This is probably why Magnus did it this way. He was trying to prevent data loss.) But, if you switch computers, this one can get lost.

So the first thing you should do for serious work is to make a new db of your own and set it as your default db. And monitor local regularly for stuff accidentally getting into local. The symptoms of a problem are that a project can't find parts of a project.

File-based databases

You can add an existing or create a new database via the appropriate buttons. Select the database name and location in the following file dialog.

MySQL databases

These work similar to the file databases, but require more parameters. Also, a MySQL server has to be installed prior to MySQL database creation. Contact your local system administrator about this.

Creating a new MySQL database might require more MySQL privileges than actually using the created database. Thus, after creation, one might want to remove the database entry via the "Remove" button (the database will continue to exist), and add it again with different MySQL privileges.