External Software and Reference Data (Outdated)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