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DyogenIBENS / Agora

Algorithm For Gene Order Reconstruction in Ancestors
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Install error #1

Closed LovellHAGSC closed 3 years ago

LovellHAGSC commented 4 years ago

Hi there, thanks for your work on Agora. I am trying to get it installed, but am getting the following error. Any help is appreciated. Cheers, John

$ bash ./checkAgoraIntegrity.sh

creates tmp directory for testing

mkdir tmp

check the preprocessing scripts

src/preprocessing/nhxGeneTrees2phylTreeGeneTrees.py example/data/GeneTreeForest.nhx.bz2 > tmp/geneTrees.protTree Traceback (most recent call last): File "src/preprocessing/nhxGeneTrees2phylTreeGeneTrees.py", line 16, in import utils.myFile as myFile ImportError: No module named utils.myFile

DyogenIBENS commented 4 years ago

Hi, thank you for using AGORA,

you have to initialize the path to the library LibsDyogen before running the script.

export PYTHONPATH="$PYTHONPATH:$PWD/LibsDyoGen"

Cheers,

Alexandra (for the dyogen team)

LovellHAGSC commented 4 years ago

Thanks! Really appreciate the quick response. I think that did the trick ... at least the program ran mostly. It produced an error though. Any thoughts about what is causing this? The directory: tmp/diags/integr/final doesn't contain a anc subdirectory. Cheers, John

Waiting ... 16 is now finished
ls: tmp/diags/integr/final/anc/: No such file or directory
 HOHOHO problems!
DyogenIBENS commented 4 years ago

I will need more information to help you. Have you installed the various libraries specified in the INSTALL file?

Could you send the complete log file of the checkAgoraIntegrity.sh bash script?

LovellHAGSC commented 4 years ago

I believe I followed the full installation instructions. Here is the log file log.txt

alouis72 commented 4 years ago

Hi, I'm very sorry for the late answer, you should try to update the code of Agora (we just fork new developments). It should be easier to install and use.

Don't hesitate to contact me if needed. Alexandra