Build and Install
- Prebuilt Binaries
- Build from Source
Pheniqs is distributed as precompiled binaries, which may be installed with package managers. It may also be built from source code. Both methods are described below.
Installing with homebrew on MacOS
Installing with conda
Stable realeases of Pheniqs are available on bioconda.
One time setup - Install Miniconda
The easiest way to do this is to head on over to Anaconda and select the correct distribution for Python3.
One time setup - Configure your Conda channels
Many groups contribute software to Conda. Each of these groups corresponds to a different channel. Bioconda is a well known channel for distributing bioinformatics software. It depends on conda-forge, another group for distributing more general software, including R and Python packages.
conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda
Simply install pheniqs using the conda package manager.
# Installs pheniqs in your 'global' conda install conda install pheniqs # Installs pheniqs in an isolated environment - recommended conda create -n pheniqs pheniqs
If you want to live on the bleeding edge, you can also install pheniqs from our anaconda channel, nyuad-cgsb.
conda install -c nyuad-cgsb pheniqs/latest
Build from Source
Pheniqs depends on HTSlib, RapidJSON and zlib. HTSLib further depends on bzip2, LZMA and optionally libdeflate for improved gzip compressed FASTQ manipulation. Pheniqs requires HTSLib version 1.8 or later and RapidJSON version 1.1.0 or later. The versions packaged in most linux distributions are very outdated and cannot be used to build Pheniqs.
Pheniqs comes bundled with a Python3 helper tool called
pheniqs-build-api.py. To build an entire virtual root of all the dependencies and compile a statically linked, portable, binary snapshot of the latest code against them simply execute
./tool/pheniqs-build-api.py build build/trunk_static.json in the code root folder. The
build folder contains several other configurations for official releases. Building with
pheniqs-build-api.py does not require elevated permissions and is ideal for building an executable on cluster environments.
% ./pheniqs-build-api.py build INFO:Package:unpacking zlib 1.2.11 INFO:Package:configuring make environment zlib 1.2.11 INFO:Package:building with make zlib 1.2.11 INFO:Package:installing with make zlib 1.2.11 INFO:Package:unpacking bz2 1.0.8 INFO:Package:building with make bz2 1.0.8 INFO:Package:installing with make bz2 1.0.8 INFO:Package:unpacking xz 5.2.5 INFO:Package:configuring make environment xz 5.2.5 INFO:Package:building with make xz 5.2.5 INFO:Package:installing with make xz 5.2.5 INFO:Package:unpacking libdeflate 1.6 INFO:Package:building with make libdeflate 1.6 INFO:Package:unpacking htslib 1.10.2 INFO:Package:configuring make environment htslib 1.10.2 INFO:Package:building with make htslib 1.10.2 INFO:Package:installing with make htslib 1.10.2 INFO:Package:unpacking rapidjson 1.1.0 INFO:Package:downloaded archive saved pheniqs git-HEAD None INFO:Package:unpacking pheniqs git-HEAD INFO:Package:building with make pheniqs git-HEAD INFO:Package:installing with make pheniqs git-HEAD
pheniqs-build-api.py is done you may inspect your binary, statically linked builds made with
pheniqs-build-api.py will also report the versions of all built in libraries.
% ./bin/static-HEAD/install/bin/pheniqs --version pheniqs version 2.0.6 zlib 1.2.11 bzlib 1.0.8 xzlib 5.2.5 libdeflate 1.6 rapidjson 1.1.0 htslib 1.10.2
You can check that your binary indeed does not link against any of the dependencies dynamically with
otool on MacOs:
% otool -L ./bin/static-HEAD/install/bin/pheniqs ./bin/static-HEAD/install/bin/pheniqs: /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 800.7.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1281.0.0)
ldd on Ubuntu:
% ldd pheniqs linux-vdso.so.1 => (0x00007ffff3300000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6910e2d000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6910b24000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f691090e000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f69106f1000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6910327000) /lib64/ld-linux-x86-64.so.2 (0x00007f69111af000)
Building with the Makefile
Pheniqs does not use automake and so does not have a configure stage. The provided Makefile will build pheniqs against existing dependencies, if they are already present. Simply execute
make && make install. You can execute
make help for some general instructions.
Dependecies on Ubuntu
All Pheniqs build dependencies are available on Ubuntu 20.04 Focal Fossa and can be installed with:
apt-get install -y \ build-essential \ rapidjson-dev \ libhts-dev \ liblzma-dev \ libdeflate-dev \ libbz2-dev
Dependecies on MacOS
All Pheniqs build dependencies are available on homebrew and can be installed with:
brew install \ zlib \ bzip2 \ rapidjson \ xz \ htslib \ libdeflate
If you want to build Pheniqs against a specific root you may provide a
PREFIX parameter, but notice that you need to specify it on each make invocation, for instance
make PREFIX=/usr/local && make install PREFIX=/usr/local. Pheniqs is regularly tested on several versions of both Clang and GCC, you can tell
make which compiler to use by setting the
CXX parameter. See travis for a comprehensive list and test results.