All pre-built binary releases can be found at GitHub .
To be able to install sequ-into on your Mac OS system, first make sure you have all support packages. It is important to add them in this order.
- Anaconda
- Download the installation package here: https://repo.angaconda.com/archive/Anaconda3-5.3.0-MacOSX-x86_64.pkg
- Open your terminal window (for example by typing "terminal" in the spotlight search field)
and enter the following:
bash ~/Downloads/Anaconda3-5.3.0-MacOSX-x86_64.sh
- The installer prompts “In order to continue the installation process, please review the license agreement.” Click
Enterto view license terms. - Scroll to the bottom of the license terms and enter
yesto agree to them. - The installer prompts you to press
Enterto confirm the location. It may take a few minutes to complete. We recommend you accept the default install location and pressEnter. - The installer prompts “Do you wish the installer to prepend the Anaconda install location to PATH in your /home/<user>/.bash_profile ?” We recommend
yes. - The installer finishes and displays “Thank you for installing Anaconda!”
- The installer describes Microsoft VS Code and asks if you would like to install VS Code. Enter
yesorno. You don't need Microsoft VS Code to use sequ-into!
If you have any trubles installing Anaconda you can review this site for more details and a visual installer: http://docs.anaconda.com/anaconda/install/mac-os/#macos-graphical-install
- Bioconda
Enter this in your terminal:
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
3. GraphMap
conda install graphmap
4. h5py
conda install -c anaconda h5py
5. pysam
conda config --add channels r conda install pysam
6. HTseq
conda install htseq
- matplotlib
To install this package with conda run one of the following:
conda install -c conda-forge matplotlib conda install -c conda-forge/label/broken matplotlib conda install -c conda-forge/label/testing matplotlib conda install -c conda-forge/label/rc matplotlib
In order to install sequ-into, go to the sequ-into repository and download the Mac OS release.
A DMG image will be downloaded. Open the image and drag the sequ-into app into your applications folder.
You are now ready to use sequ-into.
Since Microsoft Windows is the only not POSIX based operating system supported by sequ-into, a little more action must be taken.
If you have not yet installed Windows Subsystem for Linux (also known as WSL/Bash on Ubuntu/Ubuntu/...) please do so. We have prepared a guide on how to do so in the chapter :ref:`wslsetupguide` .
After you have installed WSL, we must install some dependencies that are needed by our application. Please note, the following guide is aimed at having an Ubuntu installed. However, if you have installed a different distribution, we are sure you know what you are doing and hence, you don't need detailed help ;) .
Unfortunately sequ-into depends on several smaller libraries and applications, which we now have to install.
sudo apt-get update sudo apt-get install git build-essential python3 python3-pip libhdf5-serial-dev sudo pip3 install pysam HTseq matplotlib h5py mkdir --parents ~/progs/ && cd ~/progs/ && git clone https://github.com/isovic/graphmap.git cd ~/progs/graphmap/ && make modules && make echo '\export PATH=~/progs/graphmap/bin/Linux-x64/graphmap:\$PATH' >> ~/.bashrc'
You will be asked to enter your WSL password when you submit your first sudo command. However, since sudo will give you administrator right in WSL, it might also be that it asks for your password everytime.
We have also created a cmd script which you can simply execute by double-clicking on the downloaded file after downloading it. This script asks you for your WSL password and will execute the above steps automatically.
The following will explain the packages and software going to be installed. Since you provided your sudo-password, you should get to know what we are doing ;) If you are not interested: congratulations, you're done!
First a basic developer package has to be installed, which is done by installing git for version control/access to repositories, build-essential to get C/C++ compilers (to build other software) and python3 for generating reads from fast5 files and making the statistics. python3-pip is the python package manager which we need to install some python packages, and finally libhdf5 is needed to access fast5 files.
Additionally we must ensure that you have graphmap installed. We thus download and install it to ~/progs/graphmap/ in your WSL.
After you have completed these steps, you are ready to use sequ-into!
We have built sequ-into as a portable app. You thus only need to place the downloaded executable at any location and can start using it!
We are not providing a binary download for Linux, since we assume that you are familiar with the command line, if your computer runs Linux. In explanation on why a software is needed can be found above at :ref:`_wslpackinstall` .
First you must clone the sequ-into repository , install with npm and finally build our tool.
git clone https://github.com/mjoppich/igem_munich_2018.git cd igem_munich_2018 npm install npm run build npm package-linux
You will find the sequ-into application in igem_munich_2018/release/ .
In order to have all python scripts running, please install the following dependencies. You may leave python3-pip out if you are using your own pip or anaconda.
sudo apt-get update sudo apt-get install git build-essential python3 python3-pip libhdf5-serial-dev sudo pip3 install pysam HTseq matplotlib h5py
You now have to install graphmap and add it to your path. This can, for instance, be done using the following commands:
mkdir --parents ~/progs/ && cd ~/progs/ && git clone https://github.com/isovic/graphmap.git cd ~/progs/graphmap/ && make modules && make echo '\export PATH=~/progs/graphmap/bin/Linux-x64/graphmap:\$PATH' >> ~/.bashrc'