1. Hanfei Sun
  2. NeoChiLin


NeoChiLin /

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About ChiLin

ChiLin is the Chinese Unicorn. It is sometimes called the dragon horse, a mythical creature that has a lot of legends and stories associated to it.

We use ChiLin for the name of our project as it has similar alphabet combination with ChIP-seq pipeline. Details please see in the http://docsmei.readthedocs.org/

Usage of ChiLin

usage: ChiLin.py [-h] {run,gen} ...

ChiLin : A clear ChIP-seq pipeline

positional arguments:
{run,gen} sub-command help
gen generate a template of config file run run pipeline using a config file
optional arguments:
-h, --help show this help message and exit

ChiLin-run: Run ChiLin pipeline using a config file

usage: ChiLin.py run [-h] -c CONFIG -t {Dnase,Histone,TF} [-m {mean}] [-p TOP_PEAKS] [--threads {1,2,3,4,5,6,7,8}] [-d STEP_END] [--debug]

optional arguments:
-h, --help show this help message and exit
-c CONFIG, --config CONFIG
 specify the config file to use
-t FACTOR_TYPE the most important option for ChiLin specify the analysis type and the shiftsize {Dnase: 50, Histone and TF:73} of MACS2
-m METHOD specify method for correlation plot
-p TOP_PEAKS specify peaks number for CEAS
--threads THREADS
 How many threads can be used
-d STEP_END specify the end step of pipeline, 1 for bowtie, 2 for macs, 3 for venn and correlation, 4 for ceas, 5 for conservation, 6 for motif, Note: if you only have bed file, start from 2
--debug debug mode

ChiLin-gen: A config template generator for ChiLin

usage: ChiLin.py gen [-h] --species {hg19,mm9}

optional arguments:
-h, --help show this help message and exit
--species SPECIES
 select a specie

3 steps to install ChiLin

1. R packages

install R, recommended the newest version in R session > install.packages('gplots') > install.packages('RColorBrewer')

2.External program

Before you run, please modify ChiLinjinja.conf.sample to up to your dependency. or run download.sh to automatically config as ChiLinjinja.conf.new We created a bash shell script download.sh to prepare all the dependent data and program for you. # cd path_to_chilin # sudo bash install.sh -p downloaddatapath # should mkdir under the chilin directory

3.Install ChiLin

In the terminal, change directory to the folder #python setup.py install # need root