documentation.tex

\chapter{Documenting a makefile for this manual}

This chapter will show you how to document (in \LaTeX) a makefile for this manual. While \LaTeX{} may look intimidating if you haven't used it before, it is fairly straightforward to use. We have created a number of tools to help you insert your makefile into this manual.



\section{How Makefile Documentation Should Look}

Notice how documentation will begin on a new page and a new page will be created at the end of the documentations. This is necessary to allow for wider margins that make the code easier to read.

\newgeometry{scale=0.85, centering}

\lstset{language=make,
	gobble=8,
	basicstyle=\small\ttfamily,
	breaklines=true,
	escapeinside={\%*}{*}}

\begin{lstlisting}
	PROJHOME=/projects2/act-plus/subjects/session1
	
	cwd=$(shell pwd)
	
	SUBJECTS=$(shell cat /projects2/act-plus/uds/good_subjects.txt)
	
	%*\lnote*export OMP_NUM_THREADS=1

\end{lstlisting}

You can break up and explain your code. For example, \lnum{1} sets the number of threads to allow \maken{} to parallelize.

\begin{lstlisting}
	export SUBJECTS_DIR=/projects2/act-plus/freesurfer
	export QA_TOOLS=/usr/local/freesurfer/QAtools_v1.1
	
	%*\lnote* export FREESURFER_SETUP = /usr/local/freesurfer/stable5_3/SetUpFreeSurfer.sh
	export RECON_ALL = /usr/local/freesurfer/stable5_3/bin/recon-all $(RECON_FLAGS)
	export TKMEDIT = /usr/local/freesurfer/stable5_3/bin/tkmedit	
	export SHELL=/bin/bash
	
	.PHONY: qa clean mostlyclean output noninteractive 
	
	noninteractive: setup freesurfer
	
	all: noninteractive
	
	output=$(SUBJECTS:%=%/mri/aparc+aseg.mgz) $(SUBJECTS:%=%/mri/brainmask.nii.gz)
	freesurfer: $(output)
	
	#recon-all $(RECON_FLAGS) -subjid  $${subj} -FLAIR $${subj}/flair.nii.gz -FLAIRpial;\
		
	qafiles=$(SUBJECTS:%=QA/%)
	
	qa: $(qafiles)
	
	QA/%: %
	source $$FREESURFER_SETUP ;\
	$(QA_TOOLS)/recon_checker -s $*
		
	%/mri/aparc+aseg.mgz: $(PROJHOME)/%/memprage/T1.nii.gz
	rm -rf `dirname $@`/IsRunning.*
	source /usr/local/freesurfer/stable5_3/SetUpFreeSurfer.sh ;\
	export SUBJECTS_DIR=$(SUBJECTS_DIR) ;\
	/usr/local/freesurfer/stable5_3/bin/recon-all -i $< -subjid $* -all ;\
	/usr/local/freesurfer/stable5_3/bin/recon-all -s $* -T2 
		$(PROJHOME)/$*/flair/Flair.nii.gz -T2pial
		
	%/mri/brainmask.nii.gz: $(SUBJECTS_DIR)/%/mri/aparc+aseg.mgz
	source /usr/local/freesurfer/stable5_3/SetUpFreeSurfer.sh ;\
	mri_convert $(SUBJECTS_DIR)/$*/mri/brainmask.mgz $@
	
	clean:
	echo rm -rf $(inputdirs)
	
	mostlyclean:
	@echo "Here I would delete things that are not necessary after all is said and done."
	
	output: 
	@echo "Nothing yet"
	
	setup: $(SUBJECTS)
	
	%:  $(PROJHOME)/%/memprage/T1.nii.gz 
	mkdir -p $@/mri/orig; \
	cp $^ $@/mri/orig; \
	cd $@/mri/orig; \
	mri_convert T1.nii.gz 001.mgz
	
	help:
	$(usage)
\end{lstlisting}