Question: (Closed) export PATH= fails...!
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gravatar for T_18
2.4 years ago by
T_1840
T_1840 wrote:

Dear all,

To run the program MCSC I need to add the diamond binary file into my executable search path. The path to the program is "/media/biosys5/bigDisk/Users/Programs/diamond"

So I tried: export PATH=$PATH:/media/biosys5/bigDisk/Users/Programs/diamond

also: export PATH=/media/biosys5/bigDisk/Users/Programs/diamond:$PATH

And even adding the first line into my .rcbash file. After all doing that calling "diamond" results in "No command 'diamond' found, did you mean:"

What am I doing wrong and how can I get this running with just calling diamond?

Thanks in advance!

unix diamond mcsc command line • 626 views
ADD COMMENTlink written 2.4 years ago by T_1840

Hello T_18!

We believe that this post does not fit the main topic of this site.

Not a bioinformatics question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.4 years ago by lakhujanivijay5.3k
export PATH=$PATH:/media/biosys5/bigDisk/Users/Programs/

PATH is only a collection of directories where bash searches for the entered command, but PATH is not the command itself, as in your example.

ADD REPLYlink written 2.4 years ago by ATpoint42k

Are you certain that /media/biosys5/bigDisk/Users/Programs/diamond is an executable?

  • What do you get if you do file /media/biosys5/bigDisk/Users/Programs/diamond?
  • If it is really an executable and if there is no execute bit set for that file (which can lead to file not found error) do chmod a+x /media/biosys5/bigDisk/Users/Programs/diamond and then try the file command again.
ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by GenoMax92k
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