Question: NCBI edirect "command not found"
1
gravatar for mmats010
3.3 years ago by
mmats01060
mmats01060 wrote:

This seems like too simple a question to ask, but I’m stuck and can’t find anything online to help.

I’m trying to run the edirect suite of tools locally my mac. To do so, I followed the installation procedure here [http://www.ncbi.nlm.nih.gov/books/NBK179288/] but when I proceed to try any commands (such as "esearch") I always get “command not found”. The README file suggests I run "PATH=$PATH:$HOME/edirect” but that does not help either. As far as I am aware, I haven’t changed any file other paths or directories as well.

Again, seems way too simple, but i cant seem to find anyone else having this problem.

Thanks,

Mike

ADD COMMENTlink modified 3.3 years ago by genomax69k • written 3.3 years ago by mmats01060
1

Can you post the output of

$ ls -lh ~/edirect
ADD REPLYlink written 3.3 years ago by genomax69k

this gave me "ls: /Users/BillyMAC/edirect: No such file or directory" but this is because i didnt want to install it in my home directory anyway.

The directory i did want to install it in is /Users/BillyMAC/Documents/Lab/edirect, and running the ls -lh /Users/BillyMAC/Documents/Lab/edirect

gives

 'total 6880
-rw-r--r--  1 BillyMAC  staff   2.5K Jan 11 10:25 README
drwxr-xr-x  4 BillyMAC  staff   136B Apr 12 14:51 aux
-rwxr-xr-x  1 BillyMAC  staff   265B Jan  8  2015 eaddress
-rwxr-xr-x  1 BillyMAC  staff   265B Mar 20  2013 econtact
-rwxr-xr-x  1 BillyMAC  staff    93K Apr  3 20:50 edirect.pl
-rwxr-xr-x  1 BillyMAC  staff   2.6K Apr 17  2013 edirutil
-rwxr-xr-x  1 BillyMAC  staff   263B Mar 20  2013 efetch
-rwxr-xr-x  1 BillyMAC  staff   264B Mar 20  2013 efilter
-rwxr-xr-x  1 BillyMAC  staff   262B Mar 20  2013 einfo
-rwxr-xr-x  1 BillyMAC  staff   262B Mar 20  2013 elink
-rwxr-xr-x  1 BillyMAC  staff   264B Mar 20  2013 enotify
-rwxr-xr-x  1 BillyMAC  staff   3.4K Nov 21 11:25 entrez-phrase-search
-rwxr-xr-x  1 BillyMAC  staff   262B Mar 20  2013 epost
-rwxr-xr-x  1 BillyMAC  staff   263B Mar 20  2013 eproxy
-rwxr-xr-x  1 BillyMAC  staff   264B Mar 20  2013 esearch
-rwxr-xr-x  1 BillyMAC  staff   263B Sep  8  2014 espell
-rwxr-xr-x  1 BillyMAC  staff   278B Feb 10  2014 esummary
-rwxr-xr-x  1 BillyMAC  staff   395B Mar 22 12:25 ftp-cp
-rwxr-xr-x  1 BillyMAC  staff   541B Mar 22 12:25 ftp-ls
-rwxr-xr-x  1 BillyMAC  staff    45B Aug 31  2014 join-into-groups-of
-rwxr-xr-x  1 BillyMAC  staff   7.1K Feb 10 17:25 nquire
-rwxr-xr-x  1 BillyMAC  staff   173B Jan 14  2015 reorder-columns
-rw-r--r--  1 BillyMAC  staff   1.9K Apr 12 17:24 setup-deps.log
-rwxr-xr-x  1 BillyMAC  staff   1.6K Apr  6 14:00 setup-deps.pl
-rwxr-xr-x  1 BillyMAC  staff   1.4K Mar 10 17:25 setup.sh
-rwxr-xr-x  1 BillyMAC  staff    69B Sep  3  2014 sort-uniq-count
-rwxr-xr-x  1 BillyMAC  staff    98B Aug 31  2014 sort-uniq-count-rank
-rwxr-xr-x  1 BillyMAC  staff    80B Jul 14  2015 word-at-a-time
-rwxr-xr-x  1 BillyMAC  staff   155B Mar 22 11:25 xtract
-rwxr-xr-x  1 BillyMAC  staff   2.9M Apr 12 17:25 xtract.Darwin
-rw-r--r--  1 BillyMAC  staff   169K Apr 10 13:25 xtract.go
-rwxr-xr-x  1 BillyMAC  staff    60K Mar 23 17:25 xtract.pl'

I think the problem is that the commands aren't being "routed" to the correct directory?

ADD REPLYlink modified 3.3 years ago by genomax69k • written 3.3 years ago by mmats01060
2
gravatar for genomax
3.3 years ago by
genomax69k
United States
genomax69k wrote:

Looks like the programs indeed are in /Users/BillyMAC/Documents/Lab/edirect.
If you set your $PATH to include that PATH=$PATH:/Users/BillyMAC/Documents/Lab/edirect you should be able to run any commands you need.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by genomax69k
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