In this work, PRUNIX, a framework for training and pruning convolutional neural networks is proposed for deployment on memristor crossbar based accelerators. PRUNIX takes into account the numerous non-ideal effects of memristor crossbars including weight quantization, state-drift, aging and stuck-at-faults. PRUNIX utilises a novel group lasso sawtooth regularization intended to improve non-ideality tolerance as well as sparsity, and a novel adaptive pruning algorithm (APA) intended to minimise accuracy loss by considering the sensitivity of different layers of a CNN to pruning. We compare our regularization and pruning methods with other standards on multiple CNN architectures, and observe an improvement of 13% test accuracy when quantization and other non-ideal effects are accounted for with an overall sparsity of 85%, which is similar to other methods.