====== 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.
  * [[https://github.com/dzerbino/velvet|velvet]]  Simply type make, and make color. Copy binaries into /home/.hub_local/bin
  * R and Rscript Already installed in the docker image.
  * [[http://ccb.jhu.edu/software/glimmer/index.shtml|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.
  * [[https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/|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 [[https://ftp.gnu.org/gnu/cpio/|here]]
  * [[https://gitlab.com/mcfrith/last|last]] Just cd into source dir and type make. Then copy all binaries into the bin folder to /home/.hub_local/bin folder.
  * [[https://mummer4.github.io/install/install.html|mummer]] Make sure to download mummer-4.0.0rc1.tar.gz file or latest version. Run configure --prefix=/home/.hub_local, make, make install
  * [[https://micans.org/mcl/index.html?sec_software|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.
  * [[http://www.clustal.org/clustal2/|clusatlw]] Download the static binary and copy it into the hub bin folder.
  * [[https://github.com/BenLangmead/bowtie2|Bowtie2]] Click on tags and then download the latest version. Unzip the file and then cp the bowtie2* files into the hub bin folder.
  * [[https://github.com/samtools/samtools/releases/|SAMtools]] Download the source file. Then ./configure --prefix=/home/.hub_local, make, make install
  * [[https://github.com/broadinstitute/picard/releases|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
  * [[https://bedtools.readthedocs.io/en/latest/content/installation.html|bedtools]] Follow the link and download the static binary and place in the hub bin folder.
  * [[https://github.com/freebayes/freebayes/tags|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 [[https://github.com/ninja-build/ninja/releases|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.
  * [[http://www.drive5.com/pilercr/|pilercr]] Download the source and then run make. Copy filercr binary to hub bin folder.
  * [[https://github.com/hyattpd/Prodigal/tags|prodigal]] Copy the latest version binary and move it to the hub bin folder.
  * [[http://hmmer.org/download.html|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)