slorado

Building CPU-only version of slorado on x86_64

For slorado CPU version, a minimum g++ version of 5.4 (available by default in Ubuntu 16) is required due to libtorch v2.0.0 we use currently. You can check your g++ version as g++ --version.

Install zlib development files needed for slow5lib:

 On Debian/Ubuntu : sudo apt-get install zlib1g-dev
 On Fedora/CentOS : sudo dnf/yum install zlib-devel

Clone the slorado repository recursively

 git clone --recursive https://github.com/BonsonW/slorado
 cd slorado

Run the script that downloads and extracts torchlib.
```
 scripts/install-torch2.sh cpu
```
Invoke make
```
 make -j
```
Check the compiled slorado version
```
 ./slorado --version
```

Custom libtorch path:
```
  make LIBTORCH_DIR=/path/to/libtorch
```
C++11 ABI (if you are using torch version with C++11 ABI):
```
  make cxx11_abi=1
```
You can optionally enable zstd support for built-in slow5lib when building slorado by invoking make zstd=1. This requires zstd 1.3 development libraries installed on your system (libzstd1-dev package for apt, libzstd-devel for yum/dnf).
If building with GCC 7 or lower, invoke make f16c=1 to optionally add SIMD support. SIMD is automatically enabled on GCC 8 and higher.

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