How to Install Software on Linux¶

Install Software From Your Distribution’s Repositories
Downloading and Unpacking a Binary Archive
Compileing From Source

Software we need¶

Quality Control¶

Alignment Software¶

Tophat2

Ways to Install Software¶

1. Install Software From Your Distribution’s Repositories¶

First Search:

sudo apt-cache policy [software_name]

$ sudo apt-cache policy fastqc
 [sudo] password for swijeratne:
 fastqc:
   Installed: (none)
   Candidate: 0.10.1+dfsg-2
   Version table:
      0.10.1+dfsg-2 0
         500 http://us.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages

Warning

Not all the Linux distributions have fastqc in their repos. If you see Unable to locate package warning you have to use other methods described in this class to install your software.

Then Install:

$ sudo apt-get install fastqc

If you see Unable to locate package massage, go to Compileing From Source and read that section first. Then, install fastqc

2. Downloading and Unpacking a Binary Archive¶

To download tophat2 binaries, from your home directory type

$ cd Software

Then,

$ wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz

$ tar -xvf tophat-2.1.0.Linux_x86_64.tar.gz

$ cd tophat-2.1.0.Linux_x86_64/ && ls -ls

To execute tophat2,

$ ./tophat2

3. Compileing From Source¶

Go back to Software directory by typing,

$ cd ../

Download sickle and and scythe

$ wget https://github.com/najoshi/sickle/archive/master.zip

or to download github repo,

$ git clone https://github.com/najoshi/sickle.git

Unzip master file if you use wget method

$ unzip master.zip

Remove master.zip from your directory

$ rm master.zip

Note

If you clone the github repo you can skip above steps

Clone scythe using “git clone” command

$ git clone https://github.com/najoshi/scythe.git

Compile sickle and scythe

$ cd sickel-master

$ make

$ ls -ls

Do the same for the scythe,

$ cd scythe

$ make all

$ ls -ls

Now, add both binaries to PATH, so you can access them anywhere,

$ sudo ln -s /home/yourusername/RNA-Seq/Software/sickel-master/sickle /usr/local/bin
$ sudo ln -s /home/yourusername/RNA-Seq/Software/scythe//scythe /usr/local/bin

Install fastqc from source¶

$ wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip

$ unzip fastqc_v0.11.3.zip

$ cd  ~/RNA-Seq/Software/FastQC  (Assuming your files inside RNA-Seq/SoftwareFastQC)

$ chmod a+x ./fastqc (make fastqc executable)

$ sudo ln -s  ~/RNA-Seq/Software/FastQC/fastqc  /usr/local/bin/fastqc (make a link to /usr/local/bin)