This class required numerous packages to download and compile. a list of software that we will need to run for the 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 after the cc = line:

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.
• MEGAHIT Download the static binary file. Unpack and copy all the files in the bin and share folders to the /home/.hub_local folders.
• MetaBat This package requires the boost library. Will need to download the source here. Unpack and then cd into the source folder. Run the bootstrap.sh script. Then run the b2 script that was created to build. Then run b2 headers. Then you will need to move the entire source folder to /home/.hub_local/. and create a link boost to the folder. Finaly cd into the MetaBat source folder. Edit the CMakeLists.txt and add the following two lines that point to the boost library just after the project line.

SET(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} "/home/.hub_local/boost")
SET(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} "/home/.hub_local/boost/lib")

Then run

mkdir build ; cd build && cmake -DCMAKE_INSTALL_PREFIX=/home/.hub_local ..
make

This will get the metabat1 and metabat2 compiled. But failed after that. Will see if the rest is needed.

• CheckM Follow link and use the pip3 install instructions using the hubpip command. Python packages numby, matplotlib are already installed.
• picard Download the latest version that will run with the version of Java on the hub. Version 2.27.4 worked on the current hub. Placed the jar file in the hub_data_share folder. To test run: java -jar picard.jar -h