how I can put tophat in path?

Question

[zizigolu]

Hi,

I am using a fedora virtualbox on windows 7 but by below code I am getting error who can tell me what I am doing wrong?

help me please

[user@localhost ~]$ bash
[user@localhost ~]$ cd /home/user/Downloads/bowtie2-2.2.9/
[user@localhost bowtie2-2.2.9]$ pwd
/home/user/Downloads/bowtie2-2.2.9
[user@localhost bowtie2-2.2.9]$ export TOP=/home/user/Downloads/tophat-2.1.1.Linux_x86_64/
[user@localhost bowtie2-2.2.9]$ echo $TOP
/home/user/Downloads/tophat-2.1.1.Linux_x86_64/
[user@localhost bowtie2-2.2.9]$ $TOP/tophat-p 8 -G af.gff3 -o 1_thout genome 1.fq
bash: /home/user/Downloads/tophat-2.1.1.Linux_x86_64//tophat-p: No such file or directory
[user@localhost bowtie2-2.2.9]$ bash
[user@localhost bowtie2-2.2.9]$ export TOP=/home/user/Downloads/tophat-2.1.1.Linux_x86_64/
[user@localhost bowtie2-2.2.9]$ echo $TOP
/home/user/Downloads/tophat-2.1.1.Linux_x86_64/
[user@localhost bowtie2-2.2.9]$ $TOP/tophat-p 8 -G af.gff3 -o 1_thout genome 1.fq
bash: /home/user/Downloads/tophat-2.1.1.Linux_x86_64//tophat-p: No such file or directory
[user@localhost bowtie2-2.2.9]$

Answer 1

[John]

Based on the error:

bash: /home/user/Downloads/tophat-2.1.1.Linux_x86_64//tophat-p: No such file or directory

You probably need a space between 'tophat' and '-p'. Or maybe just the -p.

Now if you want to put tophat in path with style, well that's a different question:

[zizigolu]

sorry does this make difference running tophat on virtual box fedora or linux itself????

[zizigolu]

sorry does this make difference running tophat on virtual box fedora or linux itself????

[ablanchetcohen]

It makes no difference.

Just use the name of the program to call it: tophat

-p is an argument to the program. There should always be a space between the call to the program, and the arguments to the program.

[zizigolu]

sorry should i do something extra for installing tophat in virtual box fedora or simply gunzip the file will suffice?

[ablanchetcohen]

Normally, unzipping the file should suffice.

You might want to add tophat to your PATH, and you might want to verify that Python2 is installed, which should be the case.

[zizigolu]

oh...python is not installed :(

[Ram]

Why use Fedora? I'd recommend Bio-Linux or Ubuntu. Bio-Linux comes with everything installed and Ubuntu has sudo apt-get install $WHATEVER_I_WANT

[zizigolu]

thank you Ram for your kindly tips

[Ram]

Also, check out if you can use yum. AFAIK, Fedora and yum work well together.

[Ram]

"Installing" is a transparent matter with Linux, unlike Windows or OS X (to a certain extent). When you install an application in linux, you essentially configure and build the application so its code is compiled as suited to your machine. Once this gets done, you get a file that you can execute (Let's call this the binary). Also, in many cases, you might even be given the binary directly/in a zip file.

Now when you execute a command, you are merely specifying the name of the binary to the Linux shell. If the binary is not found in the directory you're in at that moment, the shell has to figure out where this binary is, and then execute it. For the shell to know where the binary is, you need to add the path to the directory containing the binary to your $PATH variable. That way, the shell knows to check the directories in the $PATH variable for a binary when it is not found in the current directory.

This is how I learnt "Linux installation":

1. Download the zip archive - this is like downloading an EXE file on Windows (Fun Fact: an EXE is a self-extracting archive :) )
2. Extract the archive to a directory - this is like double-clicking the EXE file
3. Follow the instructions that come with the application to get it ready to use (You may have to configure and make) - this is the part that Windows hides from you. Rarely do you ever need to tweak this part in Windows.
4. Add the path to the binary to your $PATH variable. Better yet, include in ~/.bashrc the line that adds the directory to your $PATH. That way, it automatically adds the directory to your $PATH each time you log in. - This is kind of like creating a shortcut on your desktop.