Enable from source compilation through pipy

README.md

@@ -73,6 +73,9 @@ sudo apt-get install build-essential cmake zlib1g-dev
   ```
   conda -c bioconda bifrost
   ```
+
+  This binary is compiled to generic x86-64 architecture and does not include advanced SSE and AVX instructions.
+  See installing from source through conda for a natively compiled installation.
 
 * From source (Bifrost v1.0.4)
 
@@ -97,6 +100,27 @@ sudo apt-get install build-essential cmake zlib1g-dev
 
   If you encounter any problem during the installation, see the [Troubleshooting](#troubleshooting) section.
 
+* From source through pypi (Bifrost v1.0.4)
+
+```
+pip install bifrost-src --no-binary bifrost-src
+```
+
+This installation method compiles the code natively with all SSE and AVX instructions
+supported by your CPU architecture turned on. This installation method requires the compiler and build essentials to have
+been installed as described in the Requirements section.
+
+* From source through conda (Bifrost v1.0.4)
+
+```
+conda env create -n bifrost -f environment-linux.yml
+conda activate bifrost
+```
+
+This installation method compiles the code natively with all SSE and AVX instructions
+supported by your CPU architecture turned on. It does not require
+the compiler and build essentials described in the Requirements section.  
+
 ### Large *k*-mers
 
 The default maximum *k*-mer size supported is 31. To work with larger *k* in the binary, you must install Bifrost from source and replace *MAX_KMER_SIZE* with a larger multiple of 32. This can be done in two ways:
@@ -409,4 +433,4 @@ For any question, feedback or problem, please feel free to file an issue on this
 * The kseq library is copyrighted by Heng Li and released under the MIT license (http://lh3lh3.users.sourceforge.net/kseq.shtml)
 * The CRoaring library is Apache 2.0 licensed (https://github.com/RoaringBitmap/CRoaring)
 * The GetRSS library is Creative Commons Attribution 3.0 licensed
-* Bifrost is BSD-2 licensed [LICENSE](https://github.com/pmelsted/bifrost/blob/master/LICENSE)
+* Bifrost is BSD-2 licensed [LICENSE](https://github.com/pmelsted/bifrost/blob/master/LICENSE)

environment-linux.yml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.6
+  - pip=20.1.1
+  - zlib=1.2.11
+  - binutils=2.32
+  - gxx_linux-64=7.3.0
+  - pip:
+    - bifrost-src

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "wheel", "scikit-build", "cmake", "ninja"]

setup.py

@@ -0,0 +1,10 @@
+from skbuild import setup 
+
+setup(name='bifrost-src',
+      description='',
+      version='1.0.4',
+      data_files=[
+          ('.', ['setup.py'])
+      ],
+      )
+

src/CMakeLists.txt

@@ -30,7 +30,7 @@ else()
     message(FATAL_ERROR "zlib not found. Required for to output files")
 endif(ZLIB_FOUND)
 
-target_link_libraries(Bifrost bifrost_dynamic)
+target_link_libraries(Bifrost bifrost_static)
 
 install(TARGETS Bifrost DESTINATION bin)
 install(TARGETS bifrost_dynamic DESTINATION lib)