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Last active October 11, 2018 17:29
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  1. MarkFilus renamed this gist Oct 11, 2018. 1 changed file with 0 additions and 0 deletions.
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  4. MarkFilus revised this gist Oct 11, 2018. 3 changed files with 18 additions and 7 deletions.
    9 changes: 9 additions & 0 deletions activate.sh
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    # location on cluster: /opt/anaconda2/envs/cactus/etc/conda/activate.d/
    export old_path="$PATH"
    export old_pypath="$PYTHONPATH"
    # set a default queue
    export TOIL_TORQUE_ARGS="-q dept_24_core"
    # these last three are the most important
    export PATH="/opt/cactus/bin:$PATH"
    export PYTHONPATH="/opt/cactus:/opt/cactus/src"
    export CACTUS_BINARIES_MODE=local
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    # location on cluster: /opt/anaconda2/envs/cactus/etc/conda/deactivate.d/
    export PATH="$old_path"
    export PYTHONPATH="$old_pypath"
    unset old_path
    unset old_pypath
    unset CACTUS_BINARIES_MODE
    unset TOIL_TORQUE_ARGS
    9 changes: 2 additions & 7 deletions install_cactus.md
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    @@ -37,13 +37,8 @@ export PATH="/path/to/cactus/bin:$PATH"
    export PYTHONPATH="/path/to/cactus:/path/to/cactus/src"
    ```

    Here's the example from `/opt/anaconda2/envs/cactus/etc/conda/activate.d/activate.sh`
    ```bash
    export PATH="/opt/cactus/bin:$PATH"
    export PYTHONPATH="/opt/cactus:/opt/cactus/src"
    export CACTUS_BINARIES_MODE=local
    export TOIL_TORQUE_ARGS="-q dept_24_core"
    ```
    There's an example files below from the anaconda environment on our cluster, there's some extra stuff I put in to restore the old environment on a `source deactivate`.


    ### Note on if you don't have sudo
    Easiest way is to try to get some container software like docker, but if not try to compile for source or download from apt.
  5. MarkFilus created this gist Oct 11, 2018.
    54 changes: 54 additions & 0 deletions install_cactus.md
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    # Installing Cactus on Ubuntu 16.04
    This assumes you've already installed anaconda python (miniconda is enough and you do not need admin to install).

    Install apt dependencies
    ```bash
    sudo apt -y update
    sudo apt -y install build-essential pkg-config libbz2-dev libtokyocabinet-dev libkyototycoon-dev kyototycoon libkyotocabinet-dev
    ```
    Download from Github
    ```bash
    git clone https://github.com/ComparativeGenomicsToolkit/cactus.git
    cd cactus
    git submodule update --init --recursive
    ```
    Note: we are now in cactus directory, this is important for a few steps.

    Set up python:
    ```bash
    conda create -n cactus python=2.7 # must be python 2
    source activate cactus
    pip install --pre toil
    pip install -e . # must be in cactus directory
    export CACTUS_BINARIES_MODE=local
    export PATH="`pwd`/bin:$PATH"
    export PYTHONPATH="`pwd`:`pwd`/src"
    ```

    Compile binaries:
    ```bash
    make #run this in cactus dir. Do not use -j
    ```

    You're done. Consider adding the following block to the file `~/.conda/envs/cactus/etc/conda/activate.d/acti.sh`. (This runs every time you source the environment.)
    ```bash
    export CACTUS_BINARIES_MODE=local
    export PATH="/path/to/cactus/bin:$PATH"
    export PYTHONPATH="/path/to/cactus:/path/to/cactus/src"
    ```

    Here's the example from `/opt/anaconda2/envs/cactus/etc/conda/activate.d/activate.sh`
    ```bash
    export PATH="/opt/cactus/bin:$PATH"
    export PYTHONPATH="/opt/cactus:/opt/cactus/src"
    export CACTUS_BINARIES_MODE=local
    export TOIL_TORQUE_ARGS="-q dept_24_core"
    ```

    ### Note on if you don't have sudo
    Easiest way is to try to get some container software like docker, but if not try to compile for source or download from apt.
    Here's some things to try, I've not tested any of this:

    * you can extract a package to your home directory using a command like `apt-get download kyototycoon && dpkg -x kyototycoon_0.9.56-1build2_amd64.deb $HOME` I did not test it, but add `~/usr/lib/x86_64-linux-gnu` to `$LD_LIBRARY_PATH` and `~/usr/bin` to `$PATH`, and you should maybe get it to work without needing sudo, the only problem is you need to find all the dependencies

    * https://askubuntu.com/questions/193695/installing-packages-into-local-directory