This class required numerous packages to download and compile. a list of software that we will need to run our computing labs:

• R and Rscript Already installed in the docker image.\
• Bowtie2 Click on tags and then download the latest version. Unzip the file and then cp the bowtie2* files into the hub bin folder.
• SAMtools Download the source file. Then ./configure –prefix=/home/.hub_local, make, make install
• bedtools Follow the link and download the static binary and place in the hub bin folder.
• freebays Run git to download the source: git clone –recursive https://github.com/freebayes/freebayes.git. You will need to install meson with hubpip install meson. It requires liblzma which is here. Compile with ./configure –prefix=/home/.hub_local; make; make install. It requires ninja-build To compile ninja-build will need cmake. To compile run: cmake -Bbuild-cmake, cmake –build build-cmake. This will generate the `ninja` binary and a `build.ninja` file you can now use to build Ninja with itself. Now back in freebays install folder. Before you can run meson you need to modify the meson.build file in the source folder. Add in the following code:

lzma_include_dir = '/home/.hub_local/include'
lzma_library_dir = '/home/.hub_local/lib'

lzma_dep = cc.find_library('lzma',
                         dirs: lzma_library_dir,
                         static: static_build,
                         required: false)
if not lzma_dep.found()
  lzma_dep = cc.find_library('lzma',
                             dirs: lzma_library_dir,
                             required: false,
                             cpp_args: '-I' + lzma_include_dir)
endif

and then comment out the line “lzma_dep = dependency('liblzma', static: static_build)”. Then do: meson build/ –buildtype debug –wipe, cd build, ninja, ninja test, cp freebays binary to hub bin folder.

• pilercr Download the source and then run make. Copy filercr binary to hub bin folder.
• prodigal Copy the latest version binary and move it to the hub bin folder.
• hmmer Download the latest source. Run configure –prefix=/home/.hub_local, make, make install.