Galaxy license

What are the licensing terms for Galaxy?

Galaxy is distributed as open source under the conditions of the Academic Free License.

Purging unwanted histories and datasets

I have downloaded and installed a local instance of Galaxy. How can I get rid of unwanted histories and their associated datasets?

There are scripts available in the Galaxy distribution that make this process very simple. See our Purge Histories and Datasets page for details.

Galaxy Python version

What versions of the Python language do you support with your downloadable Galaxy source distribution?

We currently support Python 2.5 to 2.7. When you start up your Galaxy instance, the Python eggs for your platform will be automatically downloaded for you. See our Eggs page for more information.

Connect an external datasource to Galaxy

How do I connect an external datasource to Galaxy?

Adding an external datasource is quite easy, and only requires minimal work on the datasource side. For complete details on how to do this, see our DataSources page.

Adding support for a new data type

How do I implement support for a new data type in Galaxy?

For complete details on how to support a new data type, see our AddingDatatypes page.

Configuring Galaxy so a tool can properly generate an Excel file

One of my tools generates a binary excel file and the mime type is always binary, and the file extension is always "data.ext". This causes problems when the user tries to view ( click the eye icon ) or download ( click the 'save' link ). Changing the file type to "excel" doesn't help, and the user is forced to save the file on his desktop, rename the file to an XLS extension and then open it. Is there a way to force the mime type of the downloaded files ?

In your universe_wsgi.ini file add this line to [galaxy:datatypes]...

xls = galaxy.datatypes.data:Data,application/vnd.ms-excel

...and set the output format of your tool to xls.

Running a local Galaxy mirror on port 80, or through Apache

How can I run a Galaxy mirror alongside my regular web server (i.e. on port 80)?

Via a proxy connection in Apache. Instructions can be found on the Admin/Config/Apache Proxy page.

Central Galaxy server or Galaxy source distribution

Should I use the central Galaxy server environment hosted at Penn State or should I download the Galaxy source code and host it locally within my environment?

It depends upon your specifics needs. In general, we advise our customers to use the central Galaxy server, hosted by The Institute for Genomics, Proteomics and Bioinformatics at Penn State University. This environment is freely available to anyone with Internet access. Unlimited disk space is available for storing personal Galaxy histories and data. If you want to manage a local Galaxy environment, the Galaxy source distribution aims to be a "zero configuration", entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files.

Including HTTP links in a tool's help text

Is there a way to include an http link (eg <a href='foo'>foo</a> in the help text in a tool's xml file?

This is done using a restructured text syntax similar to the following line.

• .. _Screencasts: http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/GopsDesc

There is additional information on restructured text here.

Alignment Tools

Does Galaxy provide tools to concatenate only blocks that are adjacent to each other ( i.e. without any gap in the "projected" species )?

The following alignment tools available in Galaxy enable this:

• Join MAF blocks by species - this tool will take a MAF from your history and fuse MAF blocks which are genomically adjacent on all the specified species producing another MAF file

• Stitch MAF blocks given a set of genomic intervals - this tool uses a set of guide intervals that you provide and creates one fasta alignment block per interval for each desired species.

• Stitch Gene blocks given a set of coding exon intervals - this tool does the same as above, except uses coding region information (encoded in the BED format) to create one fasta alignment block per CCDs.

Tools that output HTML and Images

I have a tool that generates an html output with several images that I would like to integrate in to my local installation of galaxy. How can I reference the images in the html file? I'm planning on storing them in a subdirectory based on the output set e.g., galaxy_dist/database/files/000/dataset_56/img1.jpg

The correct way to do this is to use the files_path property of an output. For example:

   1 <command>some_command $input1 $output1 $output1.files_path </command>

The main html contents go into the file $output1 and any additional files should be placed in the directory specified by $output1.files_path; the external command will need to create this directory.

The filename index is reserved for displaying the dataset (containing the html). The files placed in $output1.files_path can be referenced in the html like

<img src="image1.jpg" >

Any other question