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Added newlines to setup script.
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TimD1 committed Aug 1, 2021
1 parent d89d7df commit 58f87c6
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions setup.sh
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
G1='\033[0;32m'
G2='\033[0m'

echo -e "${G1}installing aws s3 (for downloading datasets)${G2}"
echo -e "\n${G1}installing aws s3 (for downloading datasets)${G2}"
curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" \
-o "aws_cli_v2.zip" && \
unzip aws_cli_v2.zip && \
Expand All @@ -12,7 +12,7 @@ curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" \
rm -rf ./aws
echo -e "${G1}done!${G2}"

echo -e "${G1}downloading covid data...${G2}"
echo -e "\n${G1}downloading covid data...${G2}"
mkdir -p data/covid/fast5 && \
cd data/covid/fast5 && \
wget https://cadde.s3.climb.ac.uk/SP1-raw.tgz && \
Expand All @@ -21,14 +21,14 @@ mkdir -p data/covid/fast5 && \
cd -
echo -e "${G1}done!${G2}"

echo -e "${G1}downloading human data...${G2}"
echo -e "\n${G1}downloading human data...${G2}"
mkdir -p data/human/fast5
aws s3 --no-sign-request sync \
s3://ont-open-data/gm24385_2020.09/analysis/r9.4.1/20200914_1357_1-E11-H11_PAF27462_d3c9678e/guppy_v4.0.11_r9.4.1_hac_prom/align_unfiltered/chr19/fast5/ \
data/human/fast5
echo -e "${G1}done!${G2}"

echo -e "${G1}setting up virtual environment...${G2}"
echo -e "\n${G1}setting up virtual environment...${G2}"
python3.6 -m venv sf-venv3
source sf-venv3/bin/activate
pip install --upgrade pip
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