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MB 668 - Tom Sharpton/Maude David

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 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.
wiki/software/mb668.1710956975.txt.gz · Last modified: 2024/03/20 10:49 by keistc

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