Why does annotate give an error?

Question

[mohamadrezakeshtkar]

Hello

I want to annotate a peakfile

But

Why does the following command for annotate give the following error?

While I added the executable path. According to the figure below

Output file

Answer 1

[Pierre Lindenbaum]

this script calls for annotateRelativePosition.pl https://github.com/c-guzman/cipher-workflow-platform/blob/master/bin/homer/bin/annotatePeaks.pl#L1923 which is not in your PATH. https://opensource.com/article/17/6/set-path-linux

[mohamadrezakeshtkar]

Do you mean to add to the PATH for all files that are "not found"?

[Pierre Lindenbaum]

add to the PATH for all *directories containing an executable. It 'just' should be the /path/to/homer/bin

[mohamadrezakeshtkar]

In Figure 2, I added homer / bin to the PATH.

export PATH=$PATH:/Desktop/homer/bin

source ~/.profile

[mohamadrezakeshtkar]

Thank you for your help and guidance. My problem was solved.

[Pierre Lindenbaum]

cool, so mark the answer as accepted please. (Green mark on the left)

Answer 2

[mohamadrezakeshtkar]

The problem was that when annotatePeaks.pl wanted to call other functions in other programs from within the program, it could not do so despite placing the bin folder path. And we have to make all the contents of the bin executable globally.

Follow these steps to solve the problem:

1: In the terminal, write the following code:

gedit .bashrc

2: In the opened text editor, write the following code at the bottom of the page:

export PATH = / home / Computer username (mrkl) / ..... / bin

Then save the changes

3: Enter the following code in your terminal:

gedit .profile

In the opened text editor, write the following code at the bottom according to the path of the bin folder and then save

export PATH = / home / Computer username (mrkl) / ..... / bin

[Ram]

1. Use nano/emacs/vim - not gedit. Learn to work on the command line, gedit is a graphical editor.
2. You can add to PATH on just .bashrc, there is no need to edit your .profile (whatever that file is - I've heard of .bash_profile, but not .profile)
3. Do NOT edit PATH to be just a single location, every other program will stop working. Instead, use PATH=$PATH:/new/location. In other words, add to $PATH, don't overwrite it.

#3 is extremely important. Don't ruin your shell by overwriting the PATH variable.