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awk script for automating the other commercial software command lines

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# 15  
Old 12-01-2012
Hi Don

I am sorry I didnt get what i should do now.

I dont knw what I should change in this

Code:
/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Balaji/Desktop/grace-5.1.12/src:/home/Balaji/Desktop/smap_v2_0:/home/Balaji/Desktop/weblogo:/home/Balaji/Desktop/openeye_progrms/openeye/bin:/home/Balaji/vmd-1.9.1/bin/vmd:/home/Balaji/bin:/home/Balaji/moe2011/bin

Could you please advice and explain me.

Many Thanks
Balaji
# 16  
Old 12-01-2012
Since bash seems to be your login shell, there should be one or more lines in one of the three files:
Code:
$HOME/.bash_profile
$HOME/.bash_login
    or
$HOME/.profile

that starts with:
Code:
export PATH=

or a line that starts with
Code:
PATH=

and another line that starts with
Code:
export

and contains PATH in the list of words following export. For each of these three files that contains a command that sets PATH, comment out those lines by inserting an octothorpe (#) at the start of the line and add the following line after the first newly commented line:
Code:
export PATH=/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Balaji/Desktop/grace-5.1.12/src:/home/Balaji/Desktop/smap_v2_0:/home/Balaji/Desktop/weblogo:/home/Balaji/Desktop/openeye_progrms/openeye/bin:/home/Balaji/vmd-1.9.1/bin/vmd:/home/Balaji/bin:/home/Balaji/moe2011/bin

This should just need to be done in one of the above three files, but I have no idea how you have set up your environment. After editing those three files:
  1. Log out,
  2. log in again, and
  3. try running the command:
    Code:
    ksh eon_run.sh

    again.
# 17  
Old 12-02-2012
Hi Don

Thanks for advice.

I changed the above things in .bashrc file, logged out and after login tried

Code:
ksh eon_run.sh


It shows error as

Code:
eon is a tracked alias for /home/Balaji/Desktop/openeye_progrms/openeye/bin/eon

Kindly advice.

Many Thanks

Balaji
# 18  
Old 12-02-2012
Quote:
Originally Posted by bala06
Hi Don

Thanks for advice.

I changed the above things in .bashrc file, logged out and after login tried

Code:
ksh eon_run.sh


It shows error as

Code:
eon is a tracked alias for /home/Balaji/Desktop/openeye_progrms/openeye/bin/eon

Kindly advice.

Many Thanks

Balaji
That is not an error. It just means that you left the command:
Code:
type eon

in eon_run.sh.

It also means that you didn't remove the alias for eon, but that shouldn't affect the running of eon_run.sh.
# 19  
Old 12-02-2012
Hi Don

In the script, I kept the line.

Code:
#!/bin/ksh
echo $eon
type eon
ksh eon_run.sh


for file in shape_eon_input_[1-9].oeb.gz shape_eon_input_[1-9][[0-9].oeb.gz shape_eon_input_[1-9][0-9][0-9].oeb.gz
do      seq=${file##*_}
        seq=${seq%%.*}
        eon -dbase $file -besthits 47500 -prefix Eon-seq
done

Kindly check the script. i'm using.

Please advice.

Many Thanks
Balaji
# 20  
Old 12-02-2012
Use the script I gave you in message #2 in this thread:
Code:
#!/bin/ksh
for file in shape_eon_input_[1-9].oeb.gz shape_eon_input_[1-9][[0-9].oeb.gz shape_eon_input_[1-9][0-9][0-9].oeb.gz
do      seq=${file##*_}
        seq=${seq%%.*}
        eon -dbase $file -besthits 47000 -prefix Eon-$seq
done

# 21  
Old 12-02-2012
Hi Don

Thanks a lot for your patience, suggestions and help.

The scripts works.

Many Thanks
Balaji
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