download nanuq

Download Guide for Sequencing files from nanuq (Genome Quebec)

This section is intended to those who want to download their sequencing results from the NANUQ
sequencing plateform in command line mode and SLURM.

This mode is reserved to UNIX terminal

  1. Connect to the sequencing plateform nanuq
  2. Select your project containing your sequence files
  3. Select the tab “Ensemble lectures HiSeq”
  4. Select the librairies by clicking on the square button on the left like in the image
    below and click on the tab “Télécharger fichiers de lectures”:
  5. On the next window, click on the buttons as in the image below and then click on the button “`Télécharger“`:
  6. A window like this one will popup. Clik on “Enregistrer le fichier” and then OK
  7. You should then have a file named “`readSetLinks.zip“` in the dowload folder of your
    personnal computer. Transfer this file in your account on thoth or manitou.
  8. Connect to thoth or manitou and use the command “`unzip readSetLinks.zip“`. Then you
    will have 3 files with the same names as theses ones:

    run_wget.sh
    readSetLinks.txt
    Readme_fr.txt

    The file readSetLinks.txt contains the links to your sequencing files.

Follow the instructions in the Readme file. You can execute the bash script run_wget.sh
with the slurm command for interactive mode srun or use the slurm template below to
create your own slurm batch file. It is strongly recommended to use the later option


#!/bin/bash

#SBATCH -J nanuq_wget
#SBATCH -o nanuq_wget-%j.out
#SBATCH -c 1
#SBATCH -p small
#SBATCH –mail-type=ALL
#SBATCH –mail-user=
#SBATCH –time=1-00:00
#SBATCH –mem=5G

J_USER=
J_PASS=

echo -n “j_username=$J_USER&j_password=$J_PASS” > .tmp598745661.dat

chmod “600” .tmp598745661.dat


if [ "$(which wget)" ]
then
echo "Downloading with Wget"
wget --no-cookies -c -i readSetLinks.txt --post-file .tmp598745661.dat
rm .tmp598745661.dat
else
echo "Downloading with Curl"
xargs -n1 curl -C -J -L -d "@.tmp598745661.dat" -O < readSetLinks.txt
rm .tmp598745661.dat
fi

What you need to do is:

  • Add your email adress after the “`–mail-user=“` parameter
  • Write your nanuq login after the “`J_USER=“` parameter
  • Write your nanuq password after the “`J_PASS=“` parameter

Then submit your batch file to slurm with the command sbatch

Comments are closed.