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masuday committed Sep 5, 2019
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104 changes: 104 additions & 0 deletions GitHub.html5.txt
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(c) Tristano Ajmone, 2017, MIT License (MIT). Project's home repository:

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This template reuses source code taken from the following projects:

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https://github.com/sindresorhus/github-markdown-css

- Primer CSS: © 2016 GitHub Inc., MIT License (MIT):
http://primercss.io/
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170 changes: 170 additions & 0 deletions Makefile
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PANDOC = pandoc

TEXSRC = \
history.tex \
acknowledgment.tex \
license.tex \
genomic_files.tex \
genomic_gblup.tex \
genomic_gwas.tex \
genomic_qc.tex \
genomic_start.tex \
genomic_tuning.tex \
installation_availability.tex \
installation_editor.tex \
installation_env.tex \
installation_linux.tex \
installation_start.tex \
installation_windows.tex \
introduction_about.tex \
introduction_condition.tex \
introduction_difference.tex \
introduction_short.tex \
largescale_issues.tex \
largescale_pcg.tex \
largescale_reliability.tex \
largescale_reml.tex \
largescale_start.tex \
mrode_c03ex031_animal_model.tex \
mrode_c03ex032_sire_model.tex \
mrode_c03ex033_reduced_animal_model.tex \
mrode_c03ex034_animal_model_with_groups.tex \
mrode_c04ex041_repeatability_model.tex \
mrode_c04ex042_common_environment.tex \
mrode_c05ex051_mt_equal_design.tex \
mrode_c05ex052_mt_missing.tex \
mrode_c05ex053_mt_unequal_design.tex \
mrode_c05ex054_mt_no_covariance.tex \
mrode_c07ex071_maternal.tex \
mrode_c08ex081_social_interaction.tex \
mrode_c09ex091_fixed_regression.tex \
mrode_c09ex092_random_regression.tex \
mrode_c10ex102_marker_information.tex \
mrode_c10ex103_qtl.tex \
mrode_c11ex111_fixed_snp.tex \
mrode_c11ex112_mixed_snp.tex \
mrode_c11ex113_gblup.tex \
mrode_c11ex115_polygenic.tex \
mrode_c11ex116_ssgblup.tex \
mrode_c12ex121_dominance.tex \
mrode_c12ex123_dominance_inverse.tex \
mrode_c13ex131_threshold.tex \
mrode_c13ex132_threshold_linear.tex \
mrode_start.tex \
quicktour_fixed.tex \
quicktour_mixed.tex \
quicktour_mt.tex \
quicktour_ssgblup.tex \
quicktour_start.tex \
references.tex \
renum_norenum.tex \
renum_advanced.tex \
renum_basic.tex \
renum_genomic.tex \
renum_mt.tex \
renum_pedigree.tex \
renum_start.tex \
vc_advanced_aireml.tex \
vc_advanced_gs.tex \
vc_aireml.tex \
vc_gs.tex

HTMLSRC = \
history.html \
acknowledgment.html \
license.html \
genomic_files.html \
genomic_gblup.html \
genomic_gwas.html \
genomic_qc.html \
genomic_start.html \
genomic_tuning.html \
installation_availability.html \
installation_editor.html \
installation_env.html \
installation_linux.html \
installation_start.html \
installation_windows.html \
introduction_about.html \
introduction_condition.html \
introduction_difference.html \
introduction_short.html \
largescale_issues.html \
largescale_pcg.html \
largescale_reliability.html \
largescale_reml.html \
largescale_start.html \
mrode_c03ex031_animal_model.html \
mrode_c03ex032_sire_model.html \
mrode_c03ex033_reduced_animal_model.html \
mrode_c03ex034_animal_model_with_groups.html \
mrode_c04ex041_repeatability_model.html \
mrode_c04ex042_common_environment.html \
mrode_c05ex051_mt_equal_design.html \
mrode_c05ex052_mt_missing.html \
mrode_c05ex053_mt_unequal_design.html \
mrode_c05ex054_mt_no_covariance.html \
mrode_c07ex071_maternal.html \
mrode_c08ex081_social_interaction.html \
mrode_c09ex091_fixed_regression.html \
mrode_c09ex092_random_regression.html \
mrode_c10ex102_marker_information.html \
mrode_c10ex103_qtl.html \
mrode_c11ex111_fixed_snp.html \
mrode_c11ex112_mixed_snp.html \
mrode_c11ex113_gblup.html \
mrode_c11ex115_polygenic.html \
mrode_c11ex116_ssgblup.html \
mrode_c12ex121_dominance.html \
mrode_c12ex123_dominance_inverse.html \
mrode_c13ex131_threshold.html \
mrode_c13ex132_threshold_linear.html \
mrode_start.html \
quicktour_fixed.html \
quicktour_mixed.html \
quicktour_mt.html \
quicktour_ssgblup.html \
quicktour_start.html \
references.html \
renum_norenum.html \
renum_advanced.html \
renum_basic.html \
renum_genomic.html \
renum_mt.html \
renum_pedigree.html \
renum_start.html \
vc_advanced_aireml.html \
vc_advanced_gs.html \
vc_aireml.html \
vc_gs.html \
index.html

.PHONY: all img clean

.SUFFIXES: .tex .md .html

all: tutorial_blupf90.pdf $(HTMLSRC) img

tutorial_blupf90.pdf: tutorial_blupf90.tex $(TEXSRC)
pdflatex -halt-on-error tutorial_blupf90
# makeindex tutorial_blupf90
pdflatex -halt-on-error tutorial_blupf90
cp tutorial_blupf90.pdf pdf/

acknowledgment.tex: acknowledgment.md
pandoc -t latex --listings -o $@ $<

.md.tex:
pandoc -t latex --top-level-division=section --listings -o $@ $<

.md.html:
# pandoc --mathjax -smart -s -t html --toc --toc-depth=2 --template Github.html5.txt -o $@ $<
pandoc --mathjax -t html --toc --toc-depth=2 --template Github.html5.txt -o $@ $<
mv $@ html/

img:
cp -p *.png html/

clean:
rm -f *~ *.html tutorial*.pdf *.aux *.log *.out *.toc *.idx [^t]*.tex pdf/*.pdf html/*.html html/*.png
49 changes: 47 additions & 2 deletions README.md
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@@ -1,2 +1,47 @@
# Blupf90TutorialStandard
A tutorial of the BLUPF90 family programs
Introduction to BLUPF90 suite programs
======================================

Written by Yutaka Masuda

Quick links
-----------

- [Index](./index.md)
- [PDF documentation](https://github.com/masuday/Blupf90TutorialStandard/releases)

How can I build the documentation?
----------------------------------

You need the following tools.

- [Pandoc](https://pandoc.org/) v2.5.0 or later
- pdfLaTeX
- Make and Bash

Simply type the `make` command in the repository on Bash, and the programs generate a PDF file in `pdf/` and HTML files in `html/`.

~~~~~
make
~~~~~

To cleanup, run `make` with the argument.

~~~~~
make clean
~~~~~

How can I modify the note?
--------------------------

### Simple way

1. Make a fork of this repository in your account.
2. Modify the file online; select the file, edit it, and commit it.
3. After the edit, make a _pull request_.
4. Wait the response.

### Another way

1. Make a branch.
2. Modify the files and commit it.
3. Make a pull request.

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