ORP Conda Install
==

These are install instructions for the new version of the ORP, that leverage conda, and include TransABySS.

## Remove old install

cd $HOME/Oyster_River_Protocol
git pull
make clean
cd ..
rm -fr $HOME/Oyster_River_Protocol

Delete stuff from `~/.profile` and `~/.bash_profile` that are related to old install

1. Install.

git clone https://github.com/macmanes-lab/Oyster_River_Protocol.git
cd Oyster_River_Protocol
make
source ~/.profile

2. change the `config.ini`. You should just have to change the user path info.

nano software/config.ini

3. Launch the conda environment

source $HOME/Oyster_River_Protocol/software/anaconda/install/bin/activate orp_v2

4. Run test dataset (you might have to change the path to `oyster.mk` depending on where you installed this new version)

cd sampledata
$HOME/Oyster_River_Protocol/oyster.mk main STRAND=RF \
MEM=15 \
CPU=8 \
READ1=test.1.fq.gz \
READ2=test.2.fq.gz \
RUNOUT=test