Missing files in previous commit/release

Makefile

@@ -5,6 +5,7 @@ DATE:=$(shell date +%d_%m_%Y)
 
 # to be adjusted in src/main_prediction.py as well
 CLASSIFIERS:=CLF_BBH_19_07_2023 CLF_BBH_19_07_2023_no_weak CLF_BBH_sNPFR_07_01_2025 CLF_BBH_NPFR_20_02_2025 CLF_BBH_NPF_10_03_2025
+CLASSIFIERS:=CLF_BBH_19_07_2023 CLF_BBH_sNPFR_07_01_2025 CLF_BBH_NPFR_20_02_2025 CLF_BBH_NPF_10_03_2025
 CLF_PATHS:=$(foreach clf,$(CLASSIFIERS),src/$(clf).pkl)
 
 ifneq (,$(wildcard bin/python))
@@ -24,6 +25,7 @@ src/CLF_BBH_sNPFR_21_01_2025.pkl: HASH = dPl6WZOE
 src/CLF_BBH_NPFR_22_01_2025.pkl: HASH = iPIbwqtk
 src/CLF_BBH_NPFR_20_02_2025.pkl: HASH = tV359AdB
 src/CLF_BBH_NPF_04_03_2025.pkl: HASH = MwQEHvB7
+src/CLF_BBH_NPF_10_03_2025.pkl: HASH = lo8kzXSK
 
 src/CLF_BBH_%.pkl:
 	@echo "the download link might have expired;"
@@ -46,6 +48,7 @@ bin/python:
 .PHONY: clean
 clean:
 	rm -rf bin include lib lib64 log pyvenv.cfg share src/__pycache__
+	rm -rf data/apptainer
 
 .PHONY: export
 export:
@@ -74,3 +77,27 @@ sNPFR:
 	sed -i -E -e "s/clf_snpfr_suffix = '.*'/clf_snpfr_suffix = 'sNPFR_$(DATE)'/" src/main_prediction.py
 	sbatch --mem-per-cpu=$(MEM)G --array=25-42 process_multiple_conditions.sh
 
+bin/larvatagger.sif:
+	mkdir -p bin
+	module load apptainer && srun $(SLURM_OPTS) apptainer build $@ docker://flaur/larvatagger:0.18.4-20230311
+
+.PHONY: embeddings
+embeddings: bin/larvatagger.sif data/maggotuba/20230129
+	sbatch -J embeddings --mem-per-cpu=$(MEM)G --array=1-24 process_multiple_conditions.sh embeddings
+
+data/maggotuba/20230129:
+	mkdir -p $@
+	wget 'https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter/-/raw/main/pretrained_models/20230129/autoencoder_config.json?ref_type=heads&inline=false' -O- > $@/autoencoder_config.json
+	# rename in a misleading way to ensure the tagging backend picks the file
+	wget 'https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter/-/raw/main/pretrained_models/20230129/best_validated_encoder.pt?ref_type=heads&inline=false' -O- > $@/retrained_encoder.pt
+
+## does not work
+.PHONY: larvatagger
+larvatagger: install.sh
+	module load Python/3.11.5 && ./install.sh --install --with-backend --experimental
+install.sh:
+	wget 'https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/main/scripts/install.sh?ref_type=heads&inline=false' -O- > $@
+	chmod +x $@
+
+mmd:
+	cd src/Latent.jl && $(MAKE)