Commit 2ffd594b authored by Carine Rey's avatar Carine Rey
Browse files

update makefile

parent 3aea5571
......@@ -28,7 +28,7 @@ push_docker:
done
# -----------------------------------------------------------------------
# Tests and experiments
# Tests
# -----------------------------------------------------------------------
.PHONY: test_simu
test_simu:
......@@ -51,24 +51,55 @@ test_val:
mv dag.dot dagtest_val.dot && \
dot -Tsvg dagtest_val.dot -o dagtest_val.svg
# -----------------------------------------------------------------------
# experiments on real data (only Besnard)
# -----------------------------------------------------------------------
.PHONY: fast_real
fast_real:
cd example && \
reviewphiltrans detection --outdir outdir_real_data --indir real_data --fast --np 4 && \
mv dag.dot dagtest_real.dot && \
dot -Tpdf dagtest_real.dot -o dagtest_real.pdf
.PHONY: real
real:
cd example && \
reviewphiltrans detection --outdir outdir_real_data --indir real_data --preview --np 4 && \
reviewphiltrans detection --outdir outdir_real_data --indir real_data --np 4 && \
mv dag.dot dagtest_real.dot && \
dot -Tpdf dagtest_real.dot -o dagtest_real.pdf
.PHONY: analyses_30Bloom
analyses_30Bloom:
# -----------------------------------------------------------------------
# experiments on threshold choices
# -----------------------------------------------------------------------
.PHONY: analyses_30Bloom_t
analyses_30Bloom_t:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30_t --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 --no-ne --no-hapc --ns 500 && \
mv dag.dot daganalyses_tiragesBloomK30_t.dot
.PHONY: analyses_263Bloom_t
analyses_263Bloom_t:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles_t --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 --no-ne --no-hapc --ns 500 && \
mv dag.dot daganalyses_263SelectedProfiles_t.dot
# -----------------------------------------------------------------------
# experiments on Ne values choices
# -----------------------------------------------------------------------
.PHONY: analyses_30Bloom_ne
analyses_30Bloom_ne:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30 --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
mv dag.dot daganalyses_tiragesBloomK30.dot
reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30_ne --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 --fast --ns 500 && \
mv dag.dot daganalyses_tiragesBloomK30_ne.dot
.PHONY: analyses_263Bloom
analyses_263Bloom:
.PHONY: analyses_263Bloom_ne
analyses_263Bloom_ne:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 && \
mv dag.dot daganalyses_263SelectedProfiles.dot
reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles_ne --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 --fast --ns 500 && \
mv dag.dot daganalyses_263SelectedProfiles_ne.dot
# -----------------------------------------------------------------------
# Cleaning and formatting
......
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