#!/bin/bash

export LSF_DOCKER_VOLUMES="/home/yeli:/home/yeli /storage1/fs1/yeli/Active:/storage1/fs1/yeli/Active /scratch1/fs1/yeli:/scratch1/fs1/yeli"
bsub -Is -q general-interactive \
     -n 2 -G compute-yeli \
     -a 'docker(quay.io/bgruening/galaxy-hicexplorer)' /bin/bash


# download cool format from
# http://neomorph.salk.edu/zhoujt/MSMO/

# raw: 
# Q: impute signal
# E: normalize to global bkg
# T: 

for i in human 
do echo $i;
for j in Astro CLA L23 L4 L5-ET L5-IT L6b L6-CT L6-IT Lamp5 MG NP ODC OPC Pvalb-BC Pvalb-ChC Sncg Sst Vip Vsc;
do echo $j;
for t in raw T E Q;
do echo $t;
wget http://neomorph.salk.edu/zhoujt/MSMO/${i}/loop/${j}/${j}/${j}.${t}.cool 
done;
done;
done;