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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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setup.py install --prefix=XXXX does not install necessary modules #39

Closed EricDeveaud closed 5 years ago

EricDeveaud commented 5 years ago

Hello,

after issuing the following command 

python setup.py install --prefix=/some/path

and test of ragout -h

I had to perform some modifications to the installation and to the main ragout python scripts in order to have the third party modules (networkx and newick) found

1) modules from the lib directory are not installed 2) ragout main script expect lib at the same level than bin. usally helper modules must go the $PREFIX/lib/python2.7/site-packages, so ragout could not find his helper modules

so to fix the installation I had to 1) manual copy $SRC/lib/networkx and $SRC/lib/newick to /some/path/lib/python2.7/site-packages 2) hack ragout to use the correct location before installation sed -i -e "s|^lib_absolute.*|lib_absolute='newick'|" bin/ragout

also sys.path.insert(0, ragout_root) is useless as there is no python modules that can be imported from this location

regards

Eric

mikolmogorov commented 5 years ago

Hello,

lib directory is only used for running Ragout locally without installation. For system integration, you should manually install the dependencies (newick and networkx) and make sure they go into the same prefix (or just use bioconda).