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| wiki:software:st591 [2023/09/27 11:38] – keistc | wiki:software:st591 [2023/09/27 14:16] (current) – keistc |
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| * [[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/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/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. | * [[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://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. No back in freebays install folder do: meson build/ --buildtype debug --wipe, cd build, ninja, ninja test, cp freebays binary to 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. | * [[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. | * [[https://github.com/hyattpd/Prodigal/tags|prodigal]] Copy the latest version binary and move it to the hub bin folder. |
