pkg_resources.ResolutionError: No script named 'seroba'

[tseemann]

I reinstalled from git (git clone seroba && cd seroba && python3 setup.py install):

% seroba

Traceback (most recent call last):
  File "/home/linuxbrew/.linuxbrew/bin/seroba", line 4, in <module>
    __import__('pkg_resources').run_script('seroba==0.1.5', 'seroba')
  File "/home/linuxbrew/.linuxbrew/opt/python3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 748, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/linuxbrew/.linuxbrew/opt/python3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1509, in run_script
    raise ResolutionError("No script named %r" % script_name)
pkg_resources.ResolutionError: No script named 'seroba'

[andrewjpage]

Starting from a blank linuxbrew system, these are the commands I ran which got seroba running:

docker pull linuxbrew/linuxbrew
docker run --rm -it linuxbrew/linuxbrew bash

brew tap homebrew/science
brew install python3 python 

echo 'PATH="/home/linuxbrew/.linuxbrew/opt/python/libexec/bin:$PATH"' >>~/.bash_profile
export PATH="/home/linuxbrew/.linuxbrew/opt/python/libexec/bin:$PATH"
echo 'import site; site.addsitedir("/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages")' >> homebrew.pth

brew install bowtie2 kmc mummer cd-hit

git clone https://github.com/sanger-pathogens/ariba.git
cd ariba
export MPLBACKEND="agg"
pip3 install .

cd ~
git clone https://github.com/sanger-pathogens/seroba.git
cd seroba
pip3 install .
seroba

Its probably not the cleanest, but hope this helps.

[tseemann]

Why do I need ariba ? And what is this magic MPLBACKED="agg" ?

[andrewjpage]

Ariba does the local assembly under the hood. The MPL environment stops matplotlib demanding you are running X. So only needed for headless servers. Andrew

On 16 Sep 2017 2:03 am, "Torsten Seemann" notifications@github.com wrote:

Why do I need ariba ? And what is this magic MPLBACKED="agg" ?

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