External Software and Reference Data (Outdated)

This is information is now in Custom installation document. Since November 2018 it's mandatory to custom install the Ricopili pipeline.

External Software Packages

You need to install the following external software packages to a location you have access to.

For a linux system, you can enter the following commands to install each package. For other machines, you will need to go to the websites above and find the binaries compatible for your machine or compile it yourself.

Liftover

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver

METAL

wget http://www.sph.umich.edu/csg/abecasis/Metal/download/Linux-metal.tar.gz

tar -xvzf Linux-metal.tar.gz

SHAPEIT

wget https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r790.RHELS_5.4.static.tar.gz

tar -xvzf shapeit.v2.r790.RHELS_5.4.static.tar.gz

IMPUTE2

wget https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.1_x86_64_static.tgz

tar -xvzf impute_v2.3.1_x86_64_static.tgz

PLINK (v1.9)

wget https://www.cog-genomics.org/static/bin/plink170320/plink_linux_x86_64.zip

unzip plink_linux_x86_64.zip

EIGENSOFT

wget http://www.hsph.harvard.edu/wp-content/uploads/sites/181/2014/05/EIG5.0.2.tar.gz

tar -xvzf EIG5.0.2.tar.gz

cd EIG5.0.2/

cd src/

You may need to edit the Makefile to specify where the correct site for LAPACK and BLAS are ***

For example, change this line:

"LAPACK = -llapack" to "LAPACK = -L/com/extra/lapack/3.5.0/lib -llapack -lblas"

where -L specifies the path to the LAPACK library.

LAPACK can be downloaded and installed from here.

Once LAPACK has been installed, run the following commands:

make clobber

make install

EAGLE

wget https://data.broadinstitute.org/alkesgroup/Eagle/downloads/Eagle_v2.3.2.tar.gz

tar -xvzf Eagle_v2.3.2.tar.gz

External reference data

Since IMPUTE2 uses the reference data, we elect to download the data from IMPUTE2's reference data webpage: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference

Choices are outlined below.

1000 Genomes Phase 3

wget https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.tgz

wget https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3_chrX.tgz

tar -xvzf 1000GP_Phase3.tgz

tar -xvzf 1000GP_Phase3_chrX.tgz

Other

Earlier reference data releases are available at: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference