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mgtools / MinPath

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
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open file test.mps.LPout error #8

Closed jolespin closed 5 months ago

jolespin commented 5 months ago

I'm using the following version: 

# MinPath (current version: 1.6)

Here's my command: 

python ../MinPath.py -ec demo.ec -report demo.ec.minpath2 -details demo.ec.minpath.details2

I'm getting the following error: 

>>>pathway-1320[PWY-6897; thiamine diphosphate salvage II] fam=5 unique-fam=2
pathway-1321[PWY-5180; toluene degradation I (aerobic) (via o-cresol)] fam=2
>>>pathway-1321[PWY-5180; toluene degradation I (aerobic) (via o-cresol)] fam=2 unique-fam=0
pathway-1322[PWY-5182; toluene degradation II (aerobic) (via 4-methylcatechol)] fam=3
>>>pathway-1322[PWY-5182; toluene degradation II (aerobic) (via 4-methylcatechol)] fam=3 unique-fam=0
pathway-1323[PWY-5181; toluene degradation III (aerobic) (via p-cresol)] fam=3
>>>pathway-1323[PWY-5181; toluene degradation III (aerobic) (via p-cresol)] fam=3 unique-fam=0
pathway-1324[PWY-5178; toluene degradation IV (aerobic) (via catechol)] fam=12
>>>pathway-1324[PWY-5178; toluene degradation IV (aerobic) (via catechol)] fam=12 unique-fam=0
pathway-1325[PWY-5179; toluene degradation V (aerobic) (via toluene-cis-diol)] fam=7
>>>pathway-1325[PWY-5179; toluene degradation V (aerobic) (via toluene-cis-diol)] fam=7 unique-fam=0
pathway-1326[PWY-5184; toluene degradation VI (anaerobic)] fam=10
>>>pathway-1326[PWY-5184; toluene degradation VI (anaerobic)] fam=10 unique-fam=0
pathway-1327[PWY-5942; trans-lycopene biosynthesis I] fam=1
>>>pathway-1327[PWY-5942; trans-lycopene biosynthesis I] fam=1 unique-fam=0
pathway-1328[PWY-7622; UDP-alpha-D-galactofuranose biosynthesis] fam=2
>>>pathway-1328[PWY-7622; UDP-alpha-D-galactofuranose biosynthesis] fam=2 unique-fam=0
pathway-1329[PWY-4821; UDP-alpha-D-xylose biosynthesis] fam=2
>>>pathway-1329[PWY-4821; UDP-alpha-D-xylose biosynthesis] fam=2 unique-fam=0
now write mps file..
original ortholog=10 found-in-the-fam-list=8 found-in-the-fam-mapped-to-pathway=8
End of PrintMPS
now run command = /Users/jolespin/Cloud/Informatics/Development/3rdParty/MinPath/glpk-4.6/examples/glpsol test.mps -o test.mps.LPout
sh: /Users/jolespin/Cloud/Informatics/Development/3rdParty/MinPath/glpk-4.6/examples/glpsol: cannot execute binary file
open file test.mps.LPout error
jolespin commented 5 months ago

nvm. I saw in the other readme that you have rebuild on non-linux machine: 

cd MinPath/glpk-4.6/
./configure
make