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mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data
http://sourceforge.net/projects/mtoolbox/?source=navbar
GNU General Public License v3.0
90 stars 38 forks source link

parts of MToolBox don't use bundled dependencies #65

Closed 0xaf1f closed 5 years ago

0xaf1f commented 6 years ago

The installation instructions make a big deal about specifying the exact versions of certain dependencies, so I installed it into a container to make sure all the versions would be fixed. However, mapExome.py actually uses /usr/bin/python instead:

/opt/mtoolbox/MToolBox$ grep -r '/usr/bin/python' *
classifier/variants_functional_annotation.old.py:#!/usr/bin/python
mapExome.py:#!/usr/bin/python

Also, I noticed that the installation fails unless I additionally set

export LIBRARY_PATH="$MTOOLBOX_ROOT/bin/zlib/lib:$LIBRARY_PATH"
export LD_RUN_PATH="$MTOOLBOX_ROOT/bin/zlib/lib:$LD_RUN_PATH"
export PKG_CONFIG_PATH="$MTOOLBOX_ROOT/bin/zlib/lib/pkgconfig:$PKG_CONFIG_PATH"
export CPATH="$MTOOLBOX_ROOT/bin/zlib/include:$CPATH"

where /opt/mtoolbox was my $MTOOLBOX_ROOT.

I noticed these problems because my container did not have Python or zlib installed, so I got errors, but this also means that, following the instructions in your installation guide, mapExome.py is always using the system Python interpreter and parts of MToolbox are being compiled with the system zlib. It might not cause any problems, but I don't think it's what you wanted.