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Installing MultiQC on Ubuntu

I am trying to install MultiQC and I am having a lot of trouble. I am on a Ubuntu virtual machine and I have sudo rights. I followed the instructions from MultiQC for a manual instruction. I did the following:

git clone https://github.com/ewels/MultiQC.git
cd MultiQC/
sudo python setup.py install

When I type multiqc --help, I get the following output, which I don't understand:

Traceback (most recent call last):
  File "/usr/local/bin/multiqc", line 4, in <module>
    import pkg_resources
 File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2749, in <module>
    working_set = WorkingSet._build_master()
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 444, in _build_master
    ws.require(__requires__)
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 725, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 628, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: backports.functools-lru-cache

I am quite confused as to what this means ( I don't use Python). Any help would be deeply appreciated.

ngs fastqc multiqc
• 14,400 views • link
updated by Phil Ewels Phil Ewels • written by m98 m98

Please use one of these options instead:

conda install -c bioconda multiqc
multiqc .

or 

pip install multiqc    # Install
multiqc .
• 1 views • link
written by GenoMax GenoMax

2 answers 

pip install multiqc --user 
~/.local/bin/multiqc ./my_qc_reports_dir/
• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

See https://multiqc.info/docs/#installing-multiqc

Before we start - a quick note that using the system-wide installation of Python is not recommended. This often causes problems and it's a little risky to mess with it. If you find yourself prepending sudoto any MultiQC commands, take a step back and think about Python virtual environments / conda instead (see below).

As said by others - it's much safer and easier to install using Conda / Docker / etc.

• 0 views • link
written by Phil Ewels Phil Ewels

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