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Posted on October 18, 2013 by biaol — No Comments ↓

Getting Started

Ths Section Is Commented Out

with the #{—- mark, a section will show up only in full version.

Dependencies

On Debian GNU/Linux based computer:

sudo apt-get install texlive texlive-xetex texlive-latex-extra texlive-fonts-extra texlive-\
extra-utils texlive-font-utils latex-beamer pgf latexmk latex-xcolor texlive-pstricks pytho\
n-pygments

Installation

compile & install the program:

cd path/to/some/folder
svn co svn+ssh://usrname@csg.bcmd.bcm.edu/nfs/usr/local/svn/tigernotes ./
svn up
sudo python3 setup.py install

Try It Out!

Run the following script and read the output

Bash

tigernotes -h
tigernotes doc -h
tigernotes slides -h
tigernotes doc demo.notes --author "John Doe" --title "Example log documentation" -f --lite
 --output d1.pdf
tigernotes doc demo.notes --author "John Doe" --title "Example log documentation" --toc --o
utput d2.pdf

Usage

Syntax

Basic formatting

▪ Emphasis symbols

“double quote”, ‘single quote’, italics, bold, bold italics, monospaced, www.google.com

sentence emphasized

▪ Raw \LaTeXe syntax

Display math: \[\hat{\beta} = (\frac{1}{n}\sum_i^n \mathbf{x}_i\mathbf{x}_i^T)^{-1} (\frac{1}{n}\sum_i^n\mathbf{x}_iy_i)\]

Inline math: $\hat{\beta} = (\frac{1}{n}\sum_i^n \mathbf{x}_i\mathbf{x}_i^T)^{-1} (\frac{1}{n}\sum_i^n\mathbf{x}_iy_i)$

\begin{align}
p(\theta|y_1 \ldots y_6) & = \frac{p(y_1 \ldots y_6|\theta) p(\theta)}{p(y_1 \dots y_6)} \
& = \frac{p(y_1|\theta) \dots p(y_6|\theta) p(\theta)}{p(y_1 \dots y_6)} \
& = \frac{1/10}{0.02} \ \ \ (10.2 < \theta < 10.4) \
& = \left{
\begin{array}{l l}
5 & \quad \text{if $10.2 < \theta < 10.4$}\
0 & \quad \text{otherwise}
\end{array} \right.
\end{align}

▪ Reference note

I visit the BCM website daily, BCM

Check out this paper : Th. Dobzhansky (1940). Speciation as a Stage in Evolutionary Divergence. The American Naturalist. doi:10.1086/280899 | www.journals.uchicago.edu/doi/abs/10.1086/280899 reference

▪ Blocks

this
is
a list block

and you can indent it further
# but not any further

so you only have to levels to go

Warning

this is a warning block

warnings ….

Note

this is a note block

Important

this is an important block

Tip

this is a tip block

Special boxes

▪ terminal output

▪ terminal command

echo "Hello, world!"

▪ languages

Bash

vtools init esp69h
chrs='X 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22'
for chr in $chrs
do
        vtools import --format cache/esp.fmt /home/HD1/ESP6900/May02/ESP6900.chr$chr.May02.
release.vcf.gz --build hg19 -j7
        echo "sleeping for 1 min ... (time to kill me if you've planned so!)"
        sleep 60
done
vtools admin --merge_samples

argsv <- commandArgs(trailingOnly = TRUE)
dat <- read.table(pipe('cat /dev/stdin'), header=TRUE, sep = "\t")
for (i in argsv) get(i)(dat)

Python

def map( fun, list ):
    nlist = []
    for item in list:
        nlist.append( fun( item ) )
    return nlist

Cpp

#include 
using namespace std;
void main()
{
  cout << "Hello World!" << endl;
}

Sql

SELECT
  kEntity, sTranType, sItemType,
  COUNT(*) AS SaleLineCount,
  SUM(mAmount) AS sum_mAmount
FROM aTranLine
WHERE
  sTranType IN
    ('CashSale','CustInvc','CustChrg','CustCred')
 AND
   bDocMain = False
 AND
   sEntity2Type = 'CustJob'
GROUP BY kEntity, sTranType, sItemType

Text

this is plain text

▪ Alternative box names

an example

print "hi"

Careful!

a message

▪ Special boxes contents from file

The file:///filename start end (or simply file:/// to include the whole file) syntax allows inclusion of contents of external file into a special box.

Figures

Support pdf, png and jpg. This is bcm logo

{$

and smaller ...

and side by side

Tables

chr	pos	sample_size_SNV	beta_x_SNV	pvalue_SNV
1	1138931	268	0.417457	0.643625
1	1179385	268	0.0731516	0.878491
1	1418004	268	-0.272227	0.464371
1	1454412	268	0.771052	0.372779
1	1670537	268	0.0178782	0.976594
1	2160304	268	0.429178	0.449485
1	2445748	268	-0.425785	0.546444
1	2461373	268	0.599755	0.490808
1	6530254	268	0.115223	0.825298

Nested Blocks

these blocks supports nesting of other blocks: list, warning, note, tip, important

nested list/list/list

this is item 1

this item 1-1

this is a list in item 1-1

and ..
still ...

keep nesting!

Ok that's enough

nested list/out

this is item 1

this is item 2

nested list/python

this is item 1

Python

print('HELLO WORLD')

this is item 2

nested list/warning

this is item 1

Warning

I am nested

this is item 2

nested warning/list

Warning

I am nested

this is item 1

this item 1-1

this is a list in item 1-1

and ..
still ...

Ok that's enough

I am a duplicate

this is item 1

this item 1-1

this is a list in item 1-1

and ..
still ...

Ok that's enough

nested warning/out

Warning

this is item 1

this is item 2

nested warning/python

Warning

this is item 1

Python

print("HELLO WORLD")

this is item 2

nested figure/list

this is a list in item 1-1

and ..
a figure here ...

Ok that's enough

Note

a figure here ...

Another Chapter

Dokuwiki Specific

hide stuff

++++ dokuwiki hidden text |

these text will be hidden, via "folded" plugin

++++

these will be hidden via "hidden" plugin. Usually I use this for codes folding

</hidden>

[BCM website]: Baylor College of Medicine, www.bcm.edu

[reference]: Th. Dobzhansky (1940). Speciation as a Stage in Evolutionary Divergence. The American Naturalist. doi:10.1086/280899 | www.journals.uchicago.edu/doi/abs/10.1086/280899

test

Getting Started

Ths Section Is Commented Out

Dependencies

Installation

Try It Out!

Usage

Syntax

Basic formatting

▪ Emphasis symbols

▪ Raw \LaTeXe syntax

▪ Reference note

▪ Blocks

Special boxes

▪ terminal output

▪ terminal command

▪ languages

▪ Alternative box names

▪ Special boxes contents from file

Figures

Tables

Nested Blocks

nested list/list/list

nested list/out

nested list/python

nested list/warning

nested warning/list

nested warning/out

nested warning/python

nested figure/list

Another Chapter

Dokuwiki Specific

hide stuff

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