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/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
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
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
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
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
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/os.py”, line 157, in makedirs
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!
As Zhibin explained you can request email@example.com 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.:
Alternatively the C3G platform has also a module for multiqc:
module use $MUGQIC_INSTALL_HOME/modulefiles
module load mugqic/MultiQC/v1.3dev
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.
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.