FORUMInstalling multiqc on compute canada
Ann asked 1 year 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:
Exception:
Traceback (most recent call last):
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/basecommand.py”, line 215, in main
status = self.run(options, args)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/commands/install.py”, line 342, in run
prefix=options.prefix_path,
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py”, line 784, in install
**kwargs
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py”, line 851, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py”, line 1064, in move_wheel_files
isolated=self.isolated,
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/wheel.py”, line 345, in move_wheel_files
clobber(source, lib_dir, True)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/wheel.py”, line 316, in clobber
ensure_dir(destdir)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py”, line 83, in ensure_dir
os.makedirs(path)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/os.py”, line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 30] Read-only file system: ‘/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/site-packages/click-6.7.dist-info’
I tried google but I couldn’t find anything. Does anyone understand this error? Thanks!

3 Answers
Best Answer
flefebvre Staff answered 1 year ago



As Zhibin explained you can request support@computecanada.ca 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 1 year 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 1 year 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 answered 1 year 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


Eloi