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:

  1. Python/3.6.4-foss-2018a
  2. SAMtools/1..3.1-foss-2016b
  3. bio/FastQC/0.151.5-Java-1.8.0_92
  4. Bowtie2/2.3.4.1-intel-2018a
Other Installs Needed:

  1. MPI - OPENMPI

    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

  2. Ray

    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

  3. Biopython/Numpy

    pip install --user biopython
  • Biopython relies heavily on numpy and auto-installs it during the biopython install

  1. BBMap Suite

    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:
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:
#!/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:

  1. Docker

    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.

  2. Singularity

    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

  1. Bowtie2

    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

  2. Samtools

    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

  3. FastQC

    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