From b7a48c1768de7cffc2279969895e19ecca2e557a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Baraa=20Orabi=20/bara=CB=90=CA=94=20=CA=95ra=CB=90bi/?= Date: Thu, 3 Nov 2022 15:02:06 -0700 Subject: [PATCH] Update README.md --- README.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/README.md b/README.md index e3a5f1f..0597649 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,37 @@ There are few scripts/stages in Freddie: - `py/freddie_cluster.py`: Clusters the reads using their canonical segmentation representation - `py/freddie_isoforms.py`: Generates consensus isoforms of each cluster and outputs them in `GTF` format +### Obtaining Gurobi license +Freddie's clustering stage (`py/freddie_cluster.py`) uses Gurobi Solver. +To use Freddie, you need to have a Gurobi license installed. +Luckily, you can obtain one for free using an academic email address: + +- Go to [https://pages.gurobi.com/registration](https://pages.gurobi.com/registration) to register an account. +Make sure to select "Academic" to obtain the free license. + +- Once you have registered and logged in to [Gurobi.com](https://www.gurobi.com/) with your account, go to [here](https://www.gurobi.com/downloads/end-user-license-agreement-academic/) to obtain an academic license code. +You need to write this license code down because Gurobi does not save it for you. + +- Install the license on your machine using the following commands: + +```bash +conda activate freddie #Freddie conda environment contains Gurobi command line programs +grbgetkey +``` + +By default, Gurobi license installer, `grbgetkey`, installs the license file to `/home/$USER/gurobi.lic`. +If you installed the license somewhere else, you need to make Freddie know where the new license is installed. +If you are going to use the supplied Snakemake file, edit the following lines in `config.yaml` file: +```yaml +gurobi: + license: /home/$USER/gurobi.lic +``` + +If you are going to use Freddie's scripts directly, make sure to modify the Bash environment variable before running `freddie_cluster.py` using the following command: +```bash +export GRB_LICENSE_FILE=/path/to/gurobi.lic +``` + ### Align ```