hpg-methyl-galaxy

Galaxy plugin of the HPG-Methyl aligner and methylation caller.

Initial configuration

1. If you want to enable user-generated genomic indices, also add the hpgmethyl_index.xml tool entry.
2. Edit hpgmethyl.xml to set-up the paths to the built-in genomic indices. Modify the indicated entries in the <command> tag.
3. Enable or disable user-generated indices or any of the built-in genomic indices commenting or uncommenting the entries in the input_gen_selector tag, as specified in the comments of the XML file.
4. Manually generate the built-in indices if they're enabled. Check the documentation of HPG-Methyl for instructions on how to generate the indices.

Warning: Genomic indices can take a large ammount of disk space. For the GRCh37 reference genome, the corresponding index size is around 237 GB. Ensure that the target filesystem has enough disk space and users have enough disk quota before enabling custom genomic index generation.

Manual installation instructions

In case you don't want to install the tool from the public toolshed, it can be installed manually:

1. Download the latest relase of the plugin from the Releases section.
2. Decompress the .tar.gz package to GALAXY_DIR/tools/.
3. Add the tool entries for hpgmethyl.xml to GALAXY_DIR/config/tool_config.xml.

License and contribution

HPG-Methyl and its Galaxy plugin are free software and licensed under the GNU General Public License version 2. Check the COPYING file for more information.

Contact any of the following developers for any enquiry:

• Juanma Orduña ([email protected]).
• Mariano Pérez ([email protected]).
• Ricardo Olanda ([email protected]).
• César González ([email protected]).