Existing directory 1000GP_Phase3 is not detected

[dlippold]

After installing and testing genipe as described in the documentation on http://pgxcentre.github.io/genipe/installation.html I created the directory genipe_tutorial and extracted the file 1000GP_Phase3.tgz therein as described on http://pgxcentre.github.io/genipe/tutorials/tutorial_genipe.html#genipe-tut-more-details

But the script genipe_tutorial didn't detected that the directory is already there and downloaded the huge file 1000GP_Phase3.tgz again. Even if I copy the file 1000GP_Phase3.tgz itself into the directory genipe_tutorial/ it is not detected and downloaded again.

In detail I did the following:

• Installed genipe and tested the installation
• Executed the following commands

cd wget http://statgen.org/wp-content/uploads/Softwares/genipe/supp_files/hg19.tar.bz2 wget https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.tgz

mkdir $HOME/genipe_tutorial

mkdir $HOME/genipe_tutorial/hg19 cd $HOME/genipe_tutorial/hg19 tar -jxf $HOME/hg19.tar.bz2

cd $HOME/genipe_tutorial cp ../1000GP_Phase3.tgz . tar -zxf 1000GP_Phase3.tgz

cd source $HOME/genipe_pyvenv/bin/activate genipe-tutorial

• Answer the question for preparing $HOME/genipe_tutorial with "y"
• Get the message "Downloading IMPUTE2's reference files"

Is there a workaround to avoid the downloading?

[dlippold]

After looking into the program code I noticed that one has to create a file genipe_tut_done in the directory 1000GP_Phase3 after extraction, e.g. by:

cd $HOME/genipe_tutorial touch 1000GP_Phase3/genipe_tut_done

I would suggest to test only the existence of the directory and output an error message later if one of the expected files in that directory is missing.