GASE/BWA-MEM seed-extension accelerated with GASAL2

Fixed some syntactic issues that were not compatible with ubuntu 18.04.6 in Sept. 2022 (gcc issues). This has only been tested on x86_64.

Install requirements, if not already present:

sudo apt install build-essential git libboost-all-dev

Clone the repository

git clone https://github.com/neuropathbasel/gase-gasal2

Compile GASAL2 with the following commands in gasal2 directory:

E.g. for NVIDIA RTX2070 sm_75; tested with cuda-11.4, if a specific cuda version should be employed, use e.g. /usr/local/cuda-11.4. Different cuda versions can be installed from the nividia cuda ubuntu developer repo.

cd gase-gasal2/gasal2
./configure.sh /usr/local/cuda
make GPU_SM_ARCH=sm_75 MAX_SEQ_LEN=300 N_CODE=4 N_PENALTY=1

Fixed some variable naming issues according to https://stackoverflow.com/questions/67013966/error-aligned-was-not-declared-in-this-scope-and-error-expected-before

Replaced all __aligned__ with aligned_a.

Compile GASE/BWA-MEM with:

cd ..
make