#!/bin/bash  

echo "X X X X X X The process takes around 10mins to complete X X X X X X"
# define resource
resource=alliance_genome

# add the time stamped folder
cd /data/projects/glygen/downloads/$resource/

new_dir=$(date +%Y_%m_%d)/
mkdir $new_dir

# download files to new folder
cd /data/projects/glygen/downloads/$resource/$new_dir
wget -b -q -O mouse_disease_genome_alliance.tsv.gz --user-agent="Mozilla" "https://fms.alliancegenome.org/download/DISEASE-ALLIANCE_MGI.tsv.gz"
sleep 5 &&
wget -b -q -O rat_disease_genome_alliance.tsv.gz --user-agent="Mozilla" "https://fms.alliancegenome.org/download/DISEASE-ALLIANCE_RGD.tsv.gz"&&
sleep 5 &&
wget -b -q -O fruitfly_disease_genome_alliance.tsv.gz --user-agent="Mozilla" "https://fms.alliancegenome.org/download/DISEASE-ALLIANCE_FB.tsv.gz" &&
sleep 5 &&
wget -b -q -O yeast_disease_genome_alliance.tsv.gz --user-agent="Mozilla" "https://fms.alliancegenome.org/download/DISEASE-ALLIANCE_SGD.tsv.gz" &&
sleep 5 &&
wget -b -q -O orthology_alliance_combined.tsv.gz --user-agent="Mozilla" "https://fms.alliancegenome.org/download/ORTHOLOGY-ALLIANCE_COMBINED.tsv.gz" &&

echo "MSG 1: Download completed, unzipping files."

# unzip the downloaded folder

cd /data/projects/glygen/downloads/$resource/$new_dir
gunzip *.gz &&

sleep 5 &&
echo "MSG 2: Unzipping completed. Changing folder permissions and creating softlinks"


# update new folder permissions
chmod -R 775 /data/shared/glygen/downloads/$resource/$new_dir/ &&

sleep 2 &&

# create symbolic links to the files according to species

cd /data/projects/glygen/downloads/$resource/
rm current
ln -s $new_dir current

sleep 2 &&
echo "MSG 3: Download is ready, process completed."