diff --git a/workflow/.old/apps/shell/submodules/mat_exp_frontend b/workflow/.old/apps/shell/submodules/mat_exp_frontend new file mode 100644 index 00000000..461573f2 --- /dev/null +++ b/workflow/.old/apps/shell/submodules/mat_exp_frontend @@ -0,0 +1,37 @@ +# submodule mat_exp_frontend +# # @description Run the ExpFrontend.m program +# # This submodule: +# # * Pushes into the Study template directory (ExpTemplate) +# # * Prompts the user to run ExpFrontend.m +# # * Pops out +# # NOTES: +# # * ExpFrontend.m should be or is being rewritten +# mat_exp_frontend() { +# debug "Running: ${FUNCNAME[0]}" +# cat <<-EOF +# ExpFrontend.m was made for recording into a spreadsheet +# ('StudiesDataArchive.txt') the date and files used (i.e., directory paths to the +# !!Results files used as input for Z-interaction script) for each multi-experiment study. + +# Run the front end MATLAB programs in the correct order (e.g., run front end in "exp1" +# folder to call the !!Results file for the experiment you named as exp1 in the StudyInfo.csv file) +# The GTA and pairwise, TSHeatmaps, JoinInteractions and GTF Heatmap scripts use this table +# to label results and heatmaps in a meaningful way for the user and others. +# The BackgroundSD and ZscoreJoinSD fields will be filled automatically according to user +# specifications, at a later step in the QHTCP study process. + +# COpen MATLAB and in the application navigate to each specific /Exp folder, +# call and execute ExpFrontend.m by clicking the play icon. +# Use the "Open file" function from within Matlab. +# Do not double-click on the file from the directory. +# When prompted, navigate to the ExpJobs folder and the PrintResults folder within the correct job folder. +# Repeat this for every Exp# folder depending on how many experiments are being performed. +# The Exp# folder must correspond to the StudyInfo.csv created above. +# EOF + +# script="ExpFrontend.m" +# if ! ((YES)) && +# ask "Start MATLAB to run $script? This requires a GUI."; then +# $MATLAB -nosplash -r "$script" +# fi +# } diff --git a/workflow/.old/docs/easy/EASY Manual 17_0614.odt b/workflow/.old/docs/easy/EASY Manual 17_0614.odt new file mode 100644 index 00000000..36fad5c1 Binary files /dev/null and b/workflow/.old/docs/easy/EASY Manual 17_0614.odt differ diff --git a/workflow/docs/d4197ff9557ceffd5662a7ae5e9dfc90.png b/workflow/docs/d4197ff9557ceffd5662a7ae5e9dfc90.png new file mode 100644 index 00000000..4d191dff Binary files /dev/null and b/workflow/docs/d4197ff9557ceffd5662a7ae5e9dfc90.png differ diff --git a/workflow/docs/imgs/easy/1-bad-pin-map.png b/workflow/docs/imgs/easy/1-bad-pin-map.png new file mode 100644 index 00000000..086d4c06 Binary files /dev/null and b/workflow/docs/imgs/easy/1-bad-pin-map.png differ diff --git a/workflow/docs/imgs/easy/10-contamination-view.png b/workflow/docs/imgs/easy/10-contamination-view.png new file mode 100644 index 00000000..2417d4d5 Binary files /dev/null and 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