Mercurial > repos > saharlcc > isoem2_isode2

To install IsoEM2, IsoDE2 and the FC filter

1) Follow Galaxy instructions for installing a tool from the Tool Shed

2) Download and install  IsoEM2/IsoDE2 (https://github.com/mandricigor/isoem2)

3) Install other dependencies:
- hisat2 (needed for Illumina data)
  Available at https://ccb.jhu.edu/software/hisat2/index.shtml
- prinseq
  Available at http://prinseq.sourceforge.net/
- bedtools available at
  http://bedtools.readthedocs.io/en/latest/

4) Edit isoem_wrapper.sh and IsoDE2.sh. Change tool paths to where they are installed on your system

5) Copy .loc file under tool-data directory in Galaxy

6) build hisat2 for the reference you will use for mapping

7) Edit the .loc file with paths to your reference files: GTF, Transcript to gene cluster, and mapper index).

Note: steps 6 and 7 are not needed if you will use IsoEM2 option "Use reference from the history" and not "Use a built-in reference"

8) copy the entry in the tool_data_table_conf.xml file provided in this repository to the tool_data_table_conf.xml in your Galaxy config directory
author	saharlcc
date	Sun, 04 Jun 2017 11:10:45 -0400
parents	c6d2dbdf0a4d
children