**Software Setup**
==================

Software Requirements
*********************

    The following programs must be installed and included in your path prior to running SISRS:

        * Python3 (3.6.4)
            * Biopython
            * Numpy
        * Bowtie2 (2.3.4)
        * Samtools (1.3.1)
        * BBMap Suite (37.40)
        * Ray - 2.3.2-devel
        * Ray requires a working version of MPI, even if running on a single node
        * FastQC (0.11.5) (Only if trimming)

Installations
*************

    *Before proceeding with the installation of all required prerequisite software, you must establish what type of machine you plan on running SISRS v2.0 on.*

Research Cluster / HPC - Clusters
******************************************************************

    Check for the following modules on your machine:

        i. Python/3.6.4-foss-2018a
        ii. SAMtools/1..3.1-foss-2016b
        iii. bio/FastQC/0.151.5-Java-1.8.0_92
        iv. Bowtie2/2.3.4.1-intel-2018a

    Other Installs Needed:
        i. MPI - OPENMPI

           .. code-block:: bash

               wget http://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz
               tar xzvf openmpi-2.1.1.tar.gz
               cd openmpi-2.1.1
               ./configure
               make -j4
               make install

               # pwd the current location
               pwd=$(pwd)

               # Place program into path
               echo "export PATH=$pwd/openmpi-2.1.1:$""PATH" >> ~/.bash_profile

        ii. Ray

            .. code-block:: bash

               git clone https://github.com/sebhtml/RayPlatform.git
               git clone https://github.com/sebhtml/ray.git
               cd ray
               make PREFIX=ray-build HAVE_LIBZ=y LDFLAGS="-lpthread -lz"
               make install

               # pwd the current location
               pwd=$(pwd)

               # Place program into path
               echo "export PATH=$pwd/ray-build:$""PATH" >> ~/.bash_profile

        iii. Biopython/Numpy

             .. code-block:: bash

                pip install --user biopython

            * Biopython relies heavily on numpy and auto-installs it during the biopython install

        iv. BBMap Suite

            .. code-block:: bash

               wget -O BBMap_38.51.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_38.51.tar.gz/download \
               && tar -xf BBMap_38.51.tar.gz \
               && rm BBMap_38.51.tar.gz

               # pwd the current location
               pwd=$(pwd)

               # build BBTools small C-lib
               cd bbmap/jni \
                && make -f makefile.linux

               # Place program into path
               echo "export PATH=$pwd/bbmap:$""PATH" >> ~/.bash_profile

        **After all of these things have been installed make sure that BBMap, Ray, and MPI is properly located in your path.**

        Entering these software packages into your path can be done through the last few lines under each code sample or it can be done through:
            .. code-block:: bash

               vim ~/.bash_profile
               # scroll to bottom of .bash_profile and add new line
               Export PATH='path/to/software/package:$PATH'

    Writing A Script to Use the Modules:
        .. code-block:: bash

           #!/bin/bash
           # The script should start off will all the module and then follow with the code
           module load Python/3.6.4-foss-2018a;
           module load SAMtools/1.3.1-foss-2016b;
           module load bio/FastQC/0.11.5-Java-1.8.0_92;
           module load Bowtie2/2.3.4.1-intel-2018a

           python3 ...

Docker or Singularity
******************************************

    The Schwartz Lab @ URI is proud to also offer a docker image located at:
        docker://mcconnell22/sisrs:2.0

    *This image is an interactive image and is designed for users to run commands inside of it.*

    How to use the image:

    i. Docker

       .. code-block:: bash

          docker pull mcconnell22/sisrs:2.0
          docker run -it mcconnell22/sisrs:2.0

       This will pull the docker image and then allow you to run the docker image interactively.


    ii. Singularity

        .. code-block:: bash

           singularity shell docker://mcconnell22/sisrs:2.0

        This will pull the docker image and convert it into the appropriate singularity image. It will then launch an interactive shell immediately following.

Install From Nothing
****************************************

    *Refer to the section on installing software packages on research clusters to install MPI - OPENMPI, Ray, Biopython/Numpy, and BBMap Suite*

    i. Bowtie2

       .. code-block:: bash

          wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.3.1/bowtie2-2.3.3.1-linux-x86_64.zip/download
          unzip download

          # Enter Bowtie2 into the PATH
          pwd=$(pwd)
          echo "export PATH=$pwd/bowtie2-2.3.3.1-linux-x86_64:$""PATH" >> ~/.bash_profile

    ii. Samtools

        .. code-block:: bash

           wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 && \
           tar --bzip2 -xvf htslib-1.3.2.tar.bz2

           cd htslib-1.3.2
           ./configure  --enable-plugins --prefix=$HTSLIB_INSTALL_DIR && \
           make && \
           make install && \
           cp $HTSLIB_INSTALL_DIR/lib/libhts.so* /usr/lib/

           # Or any other locations
           SAMTOOLS_INSTALL_DIR=/opt/samtools

           cd /tmp
           wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
           tar --bzip2 -xf samtools-1.3.1.tar.bz2

           cd /tmp/samtools-1.3.1
           ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR && \
           make && \
           make install

           cd /
           rm -rf /tmp/samtools-1.3.1
           ln -s $HTSLIB_INSTALL_DIR/bin/tabix /usr/bin/tabix

           # Add to the apth
           echo "export PATH=/opt/samtools/bin:$""PATH" >> ~/.bash_profile

    iii. FastQC

         .. code-block:: bash

            pwd=$(pwd)
            wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
            unzip fastqc_v0.11.5.zip
            rm fastqc_v0.11.5.zip
            chmod 755 /opt/FastQC/fastqc

            # Add to the path
            echo "export PATH=$pwd/FastQC:$""PATH" >> ~/.bash_profile