conda_virtual_env

#!/bin/bash

echo Cluster $cluster
echo Process $process
echo RunningOn $runningon
mkdir $transfer_output_files
transfer_output_files=$transfer_output_files/$cluster
echo $transfer_output_files
mkdir $transfer_output_files

echo _CONDOR_JOB_IWD $_CONDOR_JOB_IWD
echo Cluster $cluster
echo Process $process
echo RunningOn $runningon

wget -q –retry-connrefused –waitretry=10 https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh #here I get the anaconda file from squid
chmod 777 * #wget does strange things
./Anaconda2-4.3.1-Linux-x86_64.sh -b -p ./anaconda > /dev/null #install anaconda, I also add an argument to the directory name
export PATH=$PWD/anaconda/bin:$PATH
echo 'Done installing anaconda'
chmod 777 *

temp_env=temp
conda create -y -n $temp_env python=2.7 anaconda > /dev/null
source activate $temp_env

#keras stuff
conda install --yes -n $temp_env pyyaml > /dev/null
conda install --yes -n $temp_env HDF5 > /dev/null
conda install --yes -n $temp_env h5py > /dev/null
conda install --yes -n $temp_env -c rdonnelly libgpuarray > /dev/null
conda install --yes -n $temp_env -c rdonnelly pygpu > /dev/null
conda install --yes -n $temp_env -c rdonnelly theano > /dev/null
conda install --yes -n $temp_env -c conda-forge theano=0.8* > /dev/null
conda install --yes -n $temp_env -c conda-forge keras=1.2* > /dev/null
conda install --yes -n $temp_env scikit-learn=0.17* > /dev/null
conda install --yes -n $temp_env -c rdkit rdkit-postgresql > /dev/null
conda install --yes -n $temp_env -c r rpy2 > /dev/null
conda install --yes -n $temp_env -c bioconda r-prroc=1.1 > /dev/null
conda install --yes -n $temp_env -c auto croc > /dev/null
conda install --yes -n $temp_env pip > /dev/null
echo 'Done installing libraries'
chmod 777 -R ./anaconda

#get virtual-screening from github
curl -H "Authorization: token xxx" -L https://api.github.com/repos/chao1224/virtual-screening/zipball > virtual-screening-master.zip
unzip virtual-screening-master.zip > /dev/null
mv chao* virtual-screening
chmod 777 *
cp -r dataset/* virtual-screening/dataset/
echo 'Done data preparation'

#run python job
cd virtual-screening
pip install --user -e .
KERAS_BACKEND=theano \
python test/test_gpu.py >> $_CONDOR_JOB_IWD/$transfer_output_files/$process.out
echo 'Done running job'
date

source deactivate $temp_env
conda remove -n $temp_env -all