get-sequences 925 Bytes
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2
#!/bin/sh

3
echo <<EOF
4 5 6 7 8 9 10 11 12
Downloading public data

- Stanford_S22 dataset from
  Boyd, S. D., et al. Individual variation in the germline Ig gene repertoire inferred
  from variable region gene rearrangements. J Immunol, 184(12), 6986–92.

- LIL-L4 dataset from
  Giraud, Salson, et al. Fast multiclonal clusterization of V(D)J recombinations
  from high-throughput sequencing. BMC Genomics 2014, 15:409.
13
EOF
Mikaël Salson's avatar
Mikaël Salson committed
14

15 16
wget -nc -q http://www.vidjil.org/seqs/Stanford_S22.tar.gz
tar xvzf Stanford_S22.tar.gz
17

18 19
echo "Retrieving demo dataset, please be patient…"
wget -nc -q -O LIL-L4.fastq.gz https://db.vidjil.org/vidjil/patient/download/sequence_file.data_file.89a7ad1ac0e2c6fa.4c313530303132352e496f6e5870726573735f3039362e66617374712e677a.gz
20 21 22 23 24 25 26 27 28
status=$?
# wget -nc -O exits with 1 when file already exists but thit is is not an
# error and should not fail the Makefile!
if [ $status -eq 1 ]; then
    exit 0
else
    exit $status
fi

29