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INSTALL.md

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Install and Setup

Dependencies

htslib

recontig and by extension dhtslib rely on htslib. htslib relies on a handful of compression and web-access libraries: zlib, bzip2, lzma, curl, and ssl. Technically htslib can be built without some of these libraries, though to get all the benefits of recontig we recommend installing all of them.

To intall htslib dependencies:

Debian / Ubuntu
---------------

sudo apt-get update  # Ensure the package list is up to date
sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev

Note: libcurl4-openssl-dev can be used as an alternative to libcurl4-gnutls-dev.

RedHat / CentOS / Amazon Linux
---------------

sudo yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel

Alpine Linux
------------

sudo apk update  # Ensure the package list is up to date
sudo apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev

OpenSUSE
--------

sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel

MacOS
-----

brew install xz autoconf automake

You will then need to download htslib. As of now we support versions >=1.10. To install htslib:

curl https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 -o htslib-1.12.tar.bz2
tar -xjf htslib-1.12.tar.bz2
cd htslib-1.12
./configure
make 
sudo make install

Building recontig from source

Clone the repository via

git clone --recurse-submodules https://github.com/blachlylab/recontig.git

If you already have htslib 1.12 installed on your system and on your path then activate your D environment

dub build

If your htslib install is in a non-standard location

LD_LIBRARY_PATH=path/to/htslib/ LIBRARY_PATH=path/to/htslib/ dub build

Building the recontig python package

Cython and PyD

Install CPython >=3.7 here is it's not already on your system. PyD does not have shared library support for GDC, so it is recommended to install using DMD or LDC fe2.065+ Best way to get both:

pip install cython pyd

#macOS
pip3 install cython pyd

To install D run the following command to install into your home folder.

curl https://dlang.org/install.sh | bash -s ldc

To activate the D environment: source ~/dlang/ldc-*/activate

You could use dmd instead of ldc.

curl https://dlang.org/install.sh | bash -s dmd

We prefer ldc for its better performance and it is the compiler we actively test recontig with. Your results may vary.

setup.py build

If not, then we have provided an install script that will install htslib on your system or check if it was provided if the user has proper system permissions to do so. We recommend running this with the ldc. Extended information about the python package can be found here.

python setup.py build -c ldc
python setup.py install
#macos
python3 setup.py build -c ldc
python3 setup.py install

To test your install:

python -c "import recontig"
#macos
python3 -c "import recontig"