clean makefile

Makefile

@@ -45,27 +45,21 @@ test_val:
 	mv dag.dot dagtest_val.dot && \
 	dot -Tsvg dagtest_val.dot -o dagtest_val.svg
 
-test_real:
+real:
 	cd example && \
-	reviewphiltrans pipeline --outdir outdir_real_data --indir real_data --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4
+	reviewphiltrans detection --outdir outdir_real_data --indir real_data --preview --np 4
 	mv dag.dot dagtest_real.dot && \
 	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf
 
-real:
-	cd example && \
-	reviewphiltrans pipeline --outdir outdir_real_data --indir real_data --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4
-
-analyses_test:
+analyses_30Bloom:
 	cd example && \
-	reviewphiltrans pipeline --outdir outdir_analyses_test --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --preview  --np 4 && \
-	mv dag.dot daganalyses_test.dot && \
-	dot -Tpdf  daganalyses_test.dot -o daganalyses_test.pdf
+	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30 --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
+	mv dag.dot daganalyses_tiragesBloomK30.dot
 
-analyses:
+analyses_263Bloom:
 	cd example && \
-	reviewphiltrans pipeline --outdir outdir_analyses --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
-	mv dag.dot daganalyses.dot && \
-	dot -Tpdf  daganalyses.dot -o daganalyses.pdf
+	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 && \
+	mv dag.dot daganalyses_263SelectedProfiles.dot
 
 clean_test:
 	rm -r example/_bistro || exit 0