FORUMInstalling multiqc on compute canada
Ann asked 9 months ago

  • Hello, I’ve been trying to install multiqc on Cedar in order to merge my fastqc analysis and alignment logs for my 100+ samples. I  loaded up python (tried both 2.7.14 and 3.6.3 versions) and then tried installing multiqc using pip install multiqc. It starts installing but then throws an error in red:
    Traceback (most recent call last):
    File “/cvmfs/”, line 215, in main
    status =, args)
    File “/cvmfs/”, line 342, in run
    File “/cvmfs/”, line 784, in install
    File “/cvmfs/”, line 851, in install
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
    File “/cvmfs/”, line 1064, in move_wheel_files
    File “/cvmfs/”, line 345, in move_wheel_files
    clobber(source, lib_dir, True)
    File “/cvmfs/”, line 316, in clobber
    File “/cvmfs/”, line 83, in ensure_dir
    File “/cvmfs/”, line 157, in makedirs
    mkdir(name, mode)
    OSError: [Errno 30] Read-only file system: ‘/cvmfs/’
    I tried google but I couldn’t find anything. Does anyone understand this error? Thanks!

    3 Answers
    Best Answer
    flefebvre Staff answered 9 months ago

  • As Zhibin explained you can request for the install or try to install it to your home with –user:
    module load python/3.6.3
    pip install --user multiqc

    The above won’t work with the default python, i.e. without the module load.
    Then next time you want to use multiqc, e.g.:
    export PATH=$PATH:$HOME/.local/bin
    multiqc --help

    Alternatively the C3G platform has also a module for multiqc:
    export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
    module use $MUGQIC_INSTALL_HOME/modulefiles
    module load mugqic/MultiQC/v1.3dev
    multiqc --help

    Ann replied 9 months ago

    Thanks for everyone’s responses! I was able to use multiqc from the C3G platform module. On compute canada’s wiki there’s a list of modules but multiqc isn’t listed. I couldn’t find multiqc through ‘module spider’ commands either. How can I find out what other modules are available on other platforms? There are many more tools that I’m interested in that I’m hesitant to try if I can’t find it on the module list.

    zhibin Staff answered 9 months ago

  • I do not think you have permission to install to cvmfs. Maybe you can try to add “–user” to your pip command and see if you can install it into your home directory. You can also send a ticket to Compute Canada ticketing system to request to install the software.

    Eloi Mercier Staff answered 9 months ago

  • Hi Ann,
    multiQC is installed on the mugqic stack already. You can load it by typing:

    module use /cvmfs/soft.mugqic/CentOS6/modulefiles
    module load mugqic/MultiQC/v1.3dev