Install THAPBI-pycits on a bare Linux account

gistfile1.txt

virtualenv venv-THAPBI-pycits -p python2
virtualenv venv-THAPBI-pycits -p python3

source venv-THAPBI-pycits/bin/activate

python2 -m pip install -U pip setuptools
python3 -m pip install -U pip setuptools

python2 -m pip install numpy
python2 -m pip install -r requirements.txt

python3 -m pip install numpy
python3 -m pip install -r requirements.txt

python2 -m pip uninstall nose
python3 -m pip install nose -I

python2 -m pip install toolz

python2 -m pip install packaging appdirs
python2 -m pip install ipython==5.3

python2 -m pip install qiime

cd
wget https://github.com/JoseBlanca/seq_crumbs/archive/v0.1.9.tar.gz
tar -zxvf v0.1.9.tar.gz 
cd seq_crumbs-0.1.9/
python2 setup.py install

cd ~/THAPBI-pycits/
./run_pycits.py -v -i data/reads/ -p DNAMIX_S95_L001_R -r data/database.fasta -t 6 -o 2017-05-06_run_pycits_test -l 2017-05-06_run_pycits_test.log