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bioinformatics-ptp / Zanardi

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Zanardi required programs #4

Open Serenatumino opened 5 years ago

Serenatumino commented 5 years ago

I've installed Zanardi following the suggestions of zanardi's manual. I have tried to install the required programs (plink, beagle3, beagle4, fcgene and admixture) using the following command:

python Zanardi.py -­‐-­‐download=beagle3,beagle4,fcGENE,PLINK,ADMIXTURE

but i have the following problems: Python 2.7.15rc1 (default, Nov 12 2018, 14:31:15) [GCC 7.3.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

Zanardi.py
File "", line 1 Zanardi.py
^ IndentationError: unexpected indent -­‐-­‐download=beagle3,beagle4,fcGENE,PLINK,ADMIXTURE

How can I fix these problems?

Thanks in advance for your help Regards

Serena

bunop commented 5 years ago

Hi Serena,

Thank you for your interest in Zanardi. Regarding your problem, it seems that you started a python terminal sessions instead of invoking Zanardi as a program. Maybe you have pasted a wrong command line from manual. Could you try to type manually this command:

python Zanardi.py --download=beagle3,beagle4,PLINK,ADMIXTURE

(see that there are only two --, while in your command you have placed ---- and some hidden characters). However, I saw that fcGENE has moved its package to a zip file instead of tar.zg and you can't to install fcGENE properly.

@malbianco , @filippob, @nicolazzie, could you check, please?