From a55840db72694cbe2455a09cfdcf4bab5cd53106 Mon Sep 17 00:00:00 2001 From: Ben Bucior Date: Sat, 9 Feb 2019 14:44:00 -0600 Subject: [PATCH] Initialize Analysis/ directory Separating general user tools from analysis scripts (examples) for the paper --- Analysis/.gitignore | 2 ++ .../R-Utilities}/parse_json_results.R | 0 .../R-Utilities}/read_named_tables.R | 0 Analysis/README.txt | 19 +++++++++++++++++++ 4 files changed, 21 insertions(+) create mode 100644 Analysis/.gitignore rename {R => Analysis/R-Utilities}/parse_json_results.R (100%) rename {R => Analysis/R-Utilities}/read_named_tables.R (100%) create mode 100644 Analysis/README.txt diff --git a/Analysis/.gitignore b/Analysis/.gitignore new file mode 100644 index 00000000..87aa7f0c --- /dev/null +++ b/Analysis/.gitignore @@ -0,0 +1,2 @@ +Figures/ + diff --git a/R/parse_json_results.R b/Analysis/R-Utilities/parse_json_results.R similarity index 100% rename from R/parse_json_results.R rename to Analysis/R-Utilities/parse_json_results.R diff --git a/R/read_named_tables.R b/Analysis/R-Utilities/read_named_tables.R similarity index 100% rename from R/read_named_tables.R rename to Analysis/R-Utilities/read_named_tables.R diff --git a/Analysis/README.txt b/Analysis/README.txt new file mode 100644 index 00000000..0d0bff2b --- /dev/null +++ b/Analysis/README.txt @@ -0,0 +1,19 @@ +# Analysis for MOFid paper + +Analysis scripts to generate figures and stats for the manuscript + + +## Steps to reproduce figures + +1. Copy relevant MOF databases (GA hMOFs, ToBaCCo, and CoRE MOF 2019) to the Data/ directory. +2. Generate MOFid's and validation data on an HPC cluster, e.g. [Northwestern quest](https://www.it.northwestern.edu/research/user-services/quest/acknowledgment.html). + a. `Scripts/HPC/run_submit_all.sh` and wait for jobs to finish. + b. `Scripts/HPC/run_post_submit_all.sh` to collect results and run the validator. +3. TODO: probably something with `Python/convert_smi_to_tables.py` +4. TODO: scripts in this directory for analysis + + +## Other comments + +Analysis scripts will live here. More general-purpose utilities are in the /bin, /Python, and /Scripts directories. +