From 62415b2f5627ab1b8ba4d924e8475a993c36d481 Mon Sep 17 00:00:00 2001 From: Pariksheet Nanda Date: Thu, 23 Mar 2017 10:51:41 -0400 Subject: [PATCH] DOC: Add `make help` usage and simplify GitHub repository name --- README.md | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a43e055..ff68ed0 100644 --- a/README.md +++ b/README.md @@ -51,12 +51,30 @@ where each well corresponds to a protein being knocked down. Usage ----- +All programs are run using a single `Makefile`. +Type the `make help` to see a list of options: + +``` sh +Usage: make [TARGET] ... + +Targets: +all (Default) Run full pipeline from image processing to plots. +help Show this help. +z-projection Generate maximum intensity projection images. +cellprofiler Collect statistics about all images. +gui-cellprofiler Interactively run CellProfiler. +stats Find significant wells from cellprofiler measurements. +clean-all Delete all output. +``` + Run the `Makefile` in this directory to generate all results. ``` sh -make +make all ``` +Depending + To tune CellProfiler's image processing, it is helpful to save results in a separate directory. One can clone this repository using a different directory name, @@ -64,7 +82,7 @@ and link to the processed image set of the original: ``` sh cd .. -git clone git@github.uconn.edu:MelloneLab/RNAi_plate_analysis_all.git rnai-screen-tf_20170314 +git clone git@github.uconn.edu:MelloneLab/rnai-screen-tf.git rnai-screen-tf_20170314 cd rnai-screen-tf_20170314 rm -rf z_projection ln -s ../../rnai-screen-tf/results/z_projection z_projection