ST591 - Tom Sharpton

This class required numerous packages to download and compile. This worked on the JH v1.0.5. a list of software that we will need to run our computing labs: NOTE: As of v1.1.3-dev, both cmake and cpio are now installed in the image.

• velvet Simply type make, and make color. Copy binaries into /home/.hub_local/bin
• R and Rscript Already installed in the docker image.
• Glimmer After unpacking. cd into the SimpleMake folder and then type make. Copy all the binaries from the bin folder to the /home/.hub_local/bin and the lib folder to the /home/.hub_local/lib folder.
• blast Download and run “configure –prefix=/home/.hub_local, then make and make install. The compilation takes a looooooong time! Around 2 hours! NOTE: will need JH instance with more than 2GB of memory to compile. Also, this requires cpio. You can download source here
• last Just cd into source dir and type make. Then copy all binaries into the bin folder to /home/.hub_local/bin folder.
• mummer Make sure to download mummer-4.0.0rc1.tar.gz file or latest version. Run configure –prefix=/home/.hub_local, make, make install
• mcl I was unable to compile the source code. So I found a way to download the Debian package: wget http://mirrors.kernel.org/ubuntu/pool/universe/m/mcl/mcl_14-137+ds-9build2_amd64.deb. Then to extract the file create a directory extracted. Then run: dpkg-deb -x mcl_14-137+ds-9build2_amd64.deb extracted/ Next copy all the files in the extracted/usr/local/bin to the /home/.hub_local/bin folder.
• clusatlw Download the static binary and copy it into the hub bin folder.
• 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
• picard Download the latest version that will run with the version of Java on the hub. Version 2.75 worked on the current hub. Placed the jar file in the hub_data_share folder. To test run: java -jar picard.jar -h
• 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 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 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.

Additionally, we'll work with the following R libraries:

• tidyverse (This is installed in the image)
• reshape2 (Install with hub.install.packages)
• phyloseq (Install with hub.install_bioconductor)