Installation Guide

Stage 1: Download and uncompress the core package

[user@host ~]$ gzip -dc CARMEN.tar.gz | tar x

[user@host ~]$ cd CARMEN

Stage 2: Download code and data for annotation module (a LARGE file, ~6GB)

[user@host ~]$ wget http://carmen.gao-lab.org/download/DeepOcean_web.tar.gz

[user@host ~]$ tar -zxvf DeepOcean_web.tar.gz

Stage 3: Setup 3rd-party toolchain

3.1 Anaconda

We recommend Anaconda2-5.0-1.

[user@host ~]$ cd ./Tools/

[user@host ~]$ wget https://repo.continuum.io/archive/Anaconda2-5.0.1-Linux-x86_64.sh

[user@host ~]$ bash Anaconda2-5.0.1-Linux-x86_64.sh

""" Do you accept the license terms? [1]yes

Anaconda2 will now be installed into this location: [2]${abs_path}+/anaconda2

Do you wish the installer to prepend the Anaconda2 install location? [3]no """

[user@host ~]$ ./anaconda2/bin/conda install mkl-rt

[user@host ~]$ ./anaconda2/bin/pip install tensorflow==1.4.0

[user@host ~]$ ./anaconda2/bin/pip install scikit-learn==0.19.1

[user@host ~]$ ./anaconda2/bin/pip install biopython

[user@host ~]$ ./anaconda2/bin/conda install -c r r=3.2.2 #INSTALL R-3.2.2

[user@host ~]$ ./anaconda2/bin/R

"Install within R"

source("http://bioconductor.org/biocLite.R")

biocLite("BSgenome.Hsapiens.UCSC.hg19")

biocLite("BSgenome.Hsapiens.UCSC.hg38")

"If you did not use the python in anaconda that we recommended, please remember to change the path of python in run-carmen.py"

3.2 Conservation via UCSC genome browse.

[user@host ~]$ wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hgWiggle

[user@host ~]$ chmod +x hgWiggle

[user@host ~]$ cd ../Conservation/

[user@host ~]$ bash Conservation_download.sh

Stage 4: Run Demo

[user@host ~]$ cd ..

[user@host ~]$ bash run-carmen_demo.sh

Congratuate if you can see output like

Finsied prediction! The prediction cost 1 mins.

Or, please just feel free to let us know by email [email protected] :)

Notes and Tips

While the core package needs ~50MB, more than 50GB space will be required eventually.

With all pre-required infrastructure set up correctly, software installation could be done in minutes.

We also recommend download conservation data and installation packages at the same time to save the installation time.

Contact:

Website: http://carmen.gao-lab.org

Email: [email protected]