General setup - wdlingit/cop GitHub Wiki

Most of my existing procedures require rackj, bowtie2, and blat. Here is an example of setting up environment in a fresh new Ubuntu20 VM.

Environment setting

ubuntu@ubuntu20:~$ mkdir Tools
ubuntu@ubuntu20:~$ cd Tools/

Download rackJ

ubuntu@ubuntu20:~/Tools$ wget https://downloads.sourceforge.net/project/rackj/0.99a/rackJ.tar.gz
ubuntu@ubuntu20:~/Tools$ tar -zxvf rackJ.tar.gz

Down related package, picard

ubuntu@ubuntu20:~/Tools$ wget https://downloads.sourceforge.net/project/picard/sam-jdk/1.89/sam-1.89.jar

Install R for ubuntu, steps from R offical website

ubuntu@ubuntu20:~/Tools$ sudo apt update -qq
ubuntu@ubuntu20:~/Tools$ sudo apt install --no-install-recommends software-properties-common dirmngr
ubuntu@ubuntu20:~/Tools$ wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
ubuntu@ubuntu20:~/Tools$ sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
ubuntu@ubuntu20:~/Tools$ sudo apt install --no-install-recommends r-base

Install bioperl, necessary perl libraries, make, and java11

ubuntu@ubuntu20:~/Tools$ sudo apt install bioperl make openjdk-11-jdk-headless
ubuntu@ubuntu20:~/Tools$ sudo cpan Statistics::Distributions
ubuntu@ubuntu20:~/Tools$ sudo cpan Statistics::R

Download bowtie2. It is OK to download any later version.

ubuntu@ubuntu20:~/Tools$ sudo apt install unzip
ubuntu@ubuntu20:~/Tools$ sudo apt install python
ubuntu@ubuntu20:~/Tools$ wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.4.4/bowtie2-2.4.4-linux-x86_64.zip
ubuntu@ubuntu20:~/Tools$ unzip bowtie2-2.4.4-linux-x86_64.zip

Download blat executable

ubuntu@ubuntu20:~/Tools$ wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
ubuntu@ubuntu20:~/Tools$ chmod 755 blat

Set PATH environment into ~/.profile

ubuntu@ubuntu20:~/Tools$ echo "PATH=\"/home/ubuntu/Tools/rackJ/scripts:\$PATH\"" >> ~/.profile
ubuntu@ubuntu20:~/Tools$ echo "PATH=\"/home/ubuntu/Tools/bowtie2-2.4.4-linux-x86_64:\$PATH\"" >> ~/.profile
ubuntu@ubuntu20:~/Tools$ echo "PATH=\"/home/ubuntu/Tools:\$PATH\"" >> ~/.profile
ubuntu@ubuntu20:~/Tools$ echo "INC=\"/home/ubuntu/Tools/rackJ/scripts/PerlLib\"" >> ~/.profile
ubuntu@ubuntu20:~/Tools$ echo "export PATH" >> ~/.profile
ubuntu@ubuntu20:~/Tools$ echo "export INC" >> ~/.profile

ubuntu@ubuntu20:~/Tools$ source ~/.profile

Ant build rackJ

In case you like to compile rackJ from the source, you need to download the source from its current repository, edit build.in.xml (copied from build.in.xml.EXAMPLE), and build it using ant.

ubuntu@ubuntu20:~/Tools$ svn checkout https://svn.code.sf.net/p/rackj/code/tags/trunk rackJ

ubuntu@ubuntu20:~/Tools/rackJ$ cat build.in.xml
<?xml version="1.0" encoding="UTF-8"?>
<project basedir="." name="setting">
		<!--MUST modify the following lines-->
		<property name="picardJAR" value="/home/ubuntu/Tools/sam-1.89.jar"/>
</project>

ubuntu@ubuntu20:~/Tools/rackJ$ ant
ubuntu@ubuntu20:~/Tools/rackJ$ ant chmod

It would be better to include the path to rackj scripts into PATH environment variable.

PATH="/home/ubuntu/Tools/rackJ/scripts:$PATH"
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