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changeo-software

Change-O

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin sequences, and reconstructing germline sequences.

Information

Usage

See which versions of changeo are available:

$ module avail changeo

Load changeo into your environment:

$ module load changeo/0.3.5

Installation

Notes from the sysadmin during installation:

$ scl enable devtoolset-2 bash
$ module load python/3.4.3
$ sudo mkdir /export/apps/changeo/0.3.5
$ sudo chown aorth /export/apps/changeo/0.3.5
$ python -m venv /export/apps/changeo/0.3.5
$ . /export/apps/changeo/0.3.5/bin/activate
$ pip install -U pip setuptools
$ pip install -U numpy scipy pandas biopython
$ pip install -U changeo
$ sudo chown -R root:root /export/apps/changeo/0.3.5

Change-O requires presto, so either install it and all of its dependencies here as well, or just make sure the Change-O module also loads presto.

changeo-software.txt · Last modified: 2017/05/31 11:29 by aorth