Install¶

Docker¶

Terminal version¶

Download Chorus:

$ docker pull forrestzhang/docker-chorus

$ docker run -v $PWD:/home/chorus -e CHORUS_USER=$USER \
  -e CHORUS_UID=$UID forrestzhang/docker-chorus -h

usage: Chorus [-h] [--version] [-j JELLYFISH] [-b BWA] -g GENOME -i INPUT
          [-s SAVED] [-p PRIMER] [-t THREADS] [-l LENGTH]
          [--homology HOMOLOGY] [-d DTM] [--docker DOCKER]

Chorus Software for Oligo FISH probe design

optional arguments:
-h, --help            show this help message and exit
--version             show program's version number and exit
-j JELLYFISH, --jellyfish JELLYFISH
                        jellyfish path
-b BWA, --bwa BWA     bwa path
-g GENOME, --genome GENOME
                        fasta format genome file
-i INPUT, --input INPUT
                        fasta format input file
-s SAVED, --save SAVED
                        result saved folder
-p PRIMER, --primer PRIMER
                        5' labeled R primer
-t THREADS, --threads THREADS
                        threads number or how may cpu you wanna use
-l LENGTH, --length LENGTH
                        probe length
--homology HOMOLOGY   homology, from 50 to 100
-d DTM, --dtm DTM     dTm, from 0 to 37
--docker DOCKER

GUI (Test Version)¶

Download Chorus:

$ docker pull forrestzhang/chorus-gui

$ docker run -i -t -p 6080:6080 -v $PWD:/home/ubuntu/Data forrestzhang/chorus-gui

Open your web browse, enter http://localhost:6080

In your web browse, open a LXTerminal

$ python3 /opt/software/Chorus/ChorusGUI.py

Manually Install¶

Ubuntu 14.04 (terminal)¶

Install dependent package

$ apt-get update && apt-get install  -y build-essential \
    cython3 \
    zlib1g-dev \
    zlibc \
    openjdk-7-jre \
    git \
    libboost-dev \
    autoconf \
    libncursesw5-dev \
    libncurses5 \
    ncurses-dev \
    libboost-thread-dev \
    python3-pip \
    samtools \
    unzip \
    python \
    curl \
    wget

Install jellyfish

$ mkdir /opt/software

$ cd /opt/software

$ wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz

$ tar zxvf jellyfish-2.2.3.tar.gz

$ mv jellyfish-2.2.3  jellyfish

$ cd jellyfish

$ ./configure && make && make install

Install bwa

$ cd /opt/software

$ git clone https://github.com/lh3/bwa.git

$ cd bwa

$ make

Install primer3-py

$ cd /opt/software

$ wget https://github.com/forrestzhang/primer3-py/archive/unicode.zip

$ unzip unicode.zip

$ cd primer3-py-unicode

$ python3 setup.py install

Download Chorus

$ cd /opt/software

$ git clone https://github.com/forrestzhang/Chorus.git

$ python3 python3 /opt/software/Chorus/Chorus.py -h



usage: Chorus [-h] [--version] [-j JELLYFISH] [-b BWA] -g GENOME -i INPUT
          [-s SAVED] [-p PRIMER] [-t THREADS] [-l LENGTH]
          [--homology HOMOLOGY] [-d DTM] [--step STEP] [--docker DOCKER]

Chorus Software for Oligo FISH probe design

optional arguments:
-h, --help            show this help message and exit
--version             show program's version number and exit
-j JELLYFISH, --jellyfish JELLYFISH
                        jellyfish path
-b BWA, --bwa BWA     bwa path
-g GENOME, --genome GENOME
                        fasta format genome file
-i INPUT, --input INPUT
                        fasta format input file
-s SAVED, --save SAVED
                        result saved folder
-p PRIMER, --primer PRIMER
                        5' labeled R primer
-t THREADS, --threads THREADS
                        threads number or how may cpu you wanna use
-l LENGTH, --length LENGTH
                        probe length
--homology HOMOLOGY   homology, from 50 to 100
-d DTM, --dtm DTM     dTm, from 0 to 37
--step STEP           step length, min=1
--docker DOCKER

Ubuntu 14.04 (GUI) Test Version¶

Install dependent package

$ apt-get update && apt-get install -y cython3  build-essential \
    zlib1g-dev \
    zlibc \
    git \
    libboost-dev \
    autoconf \
    libncursesw5-dev \
    libncurses5 \
    ncurses-dev \
    libboost-thread-dev \
    python3-pip \
    samtools \
    unzip \
    python \
    curl \
    wget \
    python3-pyqt5 \
    libfreetype6-dev \
    libxft-dev \
    python3-matplotlib

$ apt-get remove -y python3-matplotlib

Install jellyfish

$ mkdir /opt/software

$ cd /opt/software

$ wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz

$ tar zxvf jellyfish-2.2.3.tar.gz

$ mv jellyfish-2.2.3  jellyfish

$ cd jellyfish

$ ./configure && make && make install

Install bwa

$ cd /opt/software

$ git clone https://github.com/lh3/bwa.git

$ cd bwa

$ make

Install primer3-py

$ cd /opt/software

$ wget https://github.com/forrestzhang/primer3-py/archive/unicode.zip

$ unzip unicode.zip

$ cd primer3-py-unicode

$ python3 setup.py install

Install Python dependent package

$ pip3 install numpy pyfasta matplotlib

$ pip3 install pandas

Download and run Chorus

$ cd /opt/software

$ git clone https://github.com/forrestzhang/Chorus.git

$ python3 /opt/software/Chorus/ChorusGUI.py