Entering edit mode
6.9 years ago
rabio
▴
10
I have been unable to use xtract function from EDirect, as I get the following message simply by typing "xtract" into terminal:
Unable to locate xtract executable. Please execute the following: ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.Darwin.gz gunzip -f xtract.Darwin.gz chmod +x xtract.Darwin
I ran this, but it does not solve the problem. I have tried reinstalling EDirect and changing the xtract.Darwin file name to just xtract as well, but to no success. Any suggestions would be much appreciated.
Yes! And in the directory ~/edirect the following files exist: xtract, xtract.Darwin, and xtract.go. And giving all permissions (chmod 777) does not help either.
Is that directory in your
$PATH?export PATH=$PATH: ~/edirectecho $PATH returns the following:
Are you using an account called
username? Or did you just replace the real name with a dummy word? I assume the path is not permanently set like that. Can you open a new terminal window and doexport PATH=$PATH: ~/edirectto see if that fixes the strange multiple entry path above?Yes, just replacing it with a dummy word.
Thank you so much, that fixed the problem! It works now!
Hi, I'm having the exact same issue but having trouble understanding your proposed solution.
echo $PATH returns:
Opening a new terminal and executing:
returns:
Any help is appreciated!
That probably means the last step I mentioned in the original answer has not been executed.
What do you see when you do
ls -lh ~/edirect?Make sure there is no space between
$PATH:and directory name.Progress.
It did not return:
However, I still get the original error message from the OP and myself:
And executing this does not seem to fix the problem.
echo $PATH returns:
@genomax, I can't thank you enough for helping me work through this!
Just to confirm. You are using macOS? These executables are for macOS.
What do you get from
which xtractandxtract -h or --help?Correct. macOS High Sierra 10.13.6
which xtract returns:
xtract -h returns:
Did you ever manage to get xtract working?
I am running into the exact same problem.
I just followed the directions on same OS version and I am able to use
xtractfine.I get a warning about perl version of
xtractbeing obsolete (if I runxtract -h) but it works.