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Makefile
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Makefile
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.PHONY: all backup test
RUN_R := export R_LIBS_USER="C:/Users/Benjamin/Documents/R/win-library/3.4" && Rscript --vanilla
# Can also consider restructuring the repo, e.g. http://drivendata.github.io/cookiecutter-data-science/
# Variable tutorial: https://ftp.gnu.org/old-gnu/Manuals/make-3.79.1/html_chapter/make_6.html
all:
@echo "Sample make file for experimentation. Still needs work. Only backup implemented"
backup:
rsync -av --exclude=".*" --exclude="BigData/" --delete . ../../Box\ Sync/Projects/GitBackups/EnergyGrid
BigData/Robj/ccdc_hist_vals.Rds:
$(RUN_R) R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/csd_h2
BigData/Robj/ccdc_hist_160k.Rds:
$(RUN_R) R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/CSD-160K
BigData/ccdc_500_hist_vals.Rds:
$(RUN_R) R/save_h2_hists.R $@ BigData/500cifs-CCDC
# Process test subset of CCDC MOFs from Scotty 2017-11-07
BigData/Robj/tobacco_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/TobH2
BigData/Robj/tobacco_ch4.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/tobacco-20171114/ch4grids use_ch4
BigData/Robj/hmof_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/2500hMOF
BigData/Robj/hmof_ch4.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/Methane2500 use_ch4
BigData/Robj/all_hmof_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/AllhMOF
BigData/Robj/fine_01_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/FineGrid01AA
BigData/Robj/fine_05_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/FineGrid05AA
BigData/Robj/hmof_2500_fine05_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/2500hMOF-05AA
BigData/Robj/hmof_160k.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/Grids160K
BigData/Robj/adhoc_h2.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/AdHocGrids
BigData/Robj/adhoc_ch4.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/Mateo/EnergyGrid/AdHocCH4 use_ch4
BigData/Robj/ad_hoc.Rds:
${RUN_R} R/save_h2_hists.R $@ BigData/AdHoc
BigData/Convergence/top_20171122.Rds:
rmdir --ignore-fail-on-non-empty BigData/Convergence/top_h05_20171122/* # remove empty directories
${RUN_R} R/save_h2_hists.R $@ BigData/Convergence/top_h05_20171122
BigData/Robj/hyper_tuned.Rds: R/hyper_tuned.R Notebooks/setup_data.R
${RUN_R} $<
BigData/csd_formula.txt:
#export BABEL_DATADIR=/cygdrive/c/Users/Benjamin/AppData/Roaming/OpenBabel-2.4.1/data; \
# Need to make sure the data files have the linux line endings:
export BABEL_DATADIR=/cygdrive/c/Users/Benjamin/Git/mofid/src/ob_datadir/; \
rm $@; \
cd /cygdrive/c/Users/Benjamin/Git/EnergyGrid/BigData/cifs_from_csddata; \
obabel *.cif -ab -otxt --append "\tFORMULA" >> ../csd_formula.txt
BigData/Robj/csd_formulas.Rds: BigData/csd_formula.txt
${RUN_R} R/filter_ccdc_chemistry.R
BigData/TopCCDC/top.smi: Figs/ccdc_screening.tex
top3d=$$(tail -n +3 $< | cut -f1 -d' '); \
rm -r BigData/TopCCDC; \
mkdir BigData/TopCCDC; \
mkdir -p Test/; \
for structure in $$top3d; \
do cif="$${structure}_stripped.cif"; \
cp "BigData/cifs_from_csddata/$${cif}" BigData/TopCCDC; \
python ../mofid/Python/extract_moffles.py "BigData/TopCCDC/$${cif}" >> $@; \
done ;\
obabel $@ -O BigData/TopCCDC/top.svg