Question: Why does annotate give an error?
0
gravatar for mohamadrezakeshtkar
7 weeks ago by
mohamadrezakeshtkar0 wrote:

Hello

I want to annotate a peakfile

But

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

Fj8nBp.md.jpg

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

Fj8hjj.md.jpg

Output file

Fj86Zv.md.jpg

chip-seq annotate • 175 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by mohamadrezakeshtkar0
0
gravatar for Pierre Lindenbaum
7 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 7 weeks ago by mohamadrezakeshtkar0

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

ADD REPLYlink written 7 weeks ago by Pierre Lindenbaum133k

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

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

source ~/.profile
ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by mohamadrezakeshtkar0

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

ADD REPLYlink written 7 weeks ago by mohamadrezakeshtkar0

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

ADD REPLYlink written 7 weeks ago by Pierre Lindenbaum133k
0
gravatar for mohamadrezakeshtkar
7 weeks ago by
mohamadrezakeshtkar0 wrote:

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

ADD COMMENTlink written 7 weeks ago by mohamadrezakeshtkar0
  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.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by _r_am32k
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