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salilab / IHMValidation

Validation software for integrative models deposited to PDB
MIT License
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Redundant paths definitions #60

Closed aozalevsky closed 1 year ago

aozalevsky commented 1 year ago

Paths for tools from the molprobity and ATSAS suites are explicitly defined through environment variables. I think this is redundant since there is a generic and OS-independent way of using the PATH environment variable. 

ATSAS="" 
Molprobity_ramalyze=""
Molprobity_molprobity=""
Molprobity_clashscore=""
Molprobity_rotalyze=""
wkhtmltopdf=""

https://github.com/salilab/IHMValidation/blob/0bb8ad2a0c74924eafaa5871e9658df13becca5f/master/pyext/src/validation/molprobity.py#L65

https://github.com/salilab/IHMValidation/blob/0bb8ad2a0c74924eafaa5871e9658df13becca5f/master/pyext/src/validation/molprobity.py#L81

https://github.com/salilab/IHMValidation/blob/0bb8ad2a0c74924eafaa5871e9658df13becca5f/master/pyext/src/validation/molprobity.py#L97

https://github.com/salilab/IHMValidation/blob/0bb8ad2a0c74924eafaa5871e9658df13becca5f/master/pyext/src/validation/molprobity.py#L112

Moreover, in case of ATSAS it's a little bit misleading, since only datcmp used and not the whole ATSAS package.

https://github.com/salilab/IHMValidation/blob/0bb8ad2a0c74924eafaa5871e9658df13becca5f/master/pyext/src/validation/sas.py#L345-L346

aozalevsky commented 1 year ago

@benmwebb What do you think about this?

benmwebb commented 1 year ago

Agreed 100%, just have the OS look for these binaries in PATH.