run softwares tophat

Question

[zh.khodadadi]

i am a begginer user ,i install tophat2,bowtie2,fastqc and cufflink on desktop my 14.04 ubuntu by same these commands:

tar -zxvf tophat-2.1.1.Linux_x86_64.tar.gz
cd tophat-2.1.1.Linux_x86_64
./tophat2

when i use a command tophat2 in terminal(or name of every software) there is an error The program 'tophat2' is currently not installed. You can install it by typing:

sudo apt-get install tophat

i know that there is a problem about my path. how can i change my path that every software without need directery execute? if i get a directery such as cd "/home/user/Desktop/SOFTWARES/tophat-2.1.1.Linux_x86_64" ,softwares run but an example

tophat -r 20 test_ref reads_1.fq reads_2.fq 

an error
[2016-09-25 14:14:26] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2016-09-25 14:14:26] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
user@user-To-be-filled-by-O-E-M:~/Desktop/SOFTWARES/tophat-2.1.1.Linux_x86_64$

bowtie is in the Desktop/SOFTWARES but it doent run,What should I do??

[Sinji]

It's worth mentioning that you should consider using the Anaconda package manager to install a variety of bioinformatic programs.

This would be pretty easy to install using conda:

conda install -c bioconda tophat2

Answer 1

[ssv.bio]

Did you try one of these or both? 1) sudo apt-get install bowtie 2) sudo apt-get install bowtie2

[zh.khodadadi]

i use 2) sudo apt-get install soft name( bowtie2) and soft installed but its version was old. and i need install new version.

Answer 2

[GenoMax]

Use these directions to modify your $PATH so you can add new directories to it.

Programs may need execute bit set before they can be run (e.g. for this to work ./tophat2). You can do that by chmod a+x /path_to/tophat2

If you are serious about learning all this then spend a few hours here to get the basics of unix under your belt.