Passing arguments to interactive program through bash script, here document Post: 302909537

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Top Forums Shell Programming and Scripting Passing arguments to interactive program through bash script, here document Post 302909537 by biochemist on Thursday 17th of July 2014 01:38:01 PM

07-17-2014

Registered User

Dear Corona688,
Thank you for your reply. I incorporated the changes but it seems its not able to find the data file ( although i put explicit path name).
Below is the code and error:

Code:

#!/bin/bash                                                                  

cat <<EOF > data.txt                                                         
auto                                                                         
n                                                                            
/home/multalign/tab/dna.tab                                           
                                                                             
n                                                                            
msf                                                                          
y                                                                            
aligned                                                                      
                                                                             
100.90                                                                       
EOF                                                                          

#for x in {A..H}                                                             
for x in H
do
    echo $x
    for y in PreS1 PreS2 S X
    do
        /home/multalign/tab/ma ${x}_${y}.fas < data.txt
        echo Done: ${x}_${y}.fas
    done
done

Error:

Code:

H
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_PreS1.fas
Sequence #  30

Error: Error reading blosum62.tab. 
Done: H_PreS1.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_PreS2.fas
Sequence #  30

Error: Error reading blosum62.tab. 
Done: H_PreS2.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_S.fas
Sequence #  72

Error: Error reading blosum62.tab. 
Done: H_S.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_X.fas
Sequence #  26

Error: Error reading blosum62.tab. 
Done: H_X.fas

Thanks

biochemist

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LEARN ABOUT DEBIAN

bzexe

BZEXE(1)						      General Commands Manual							  BZEXE(1)

NAME

       bzexe - compress executable files in place

SYNOPSIS

       bzexe [ name ...  ]

DESCRIPTION

       The  bzexe  utility  allows you to compress executables in place and have them automatically uncompress and execute when you run them (at a
       penalty in performance).  For example if you execute ``bzexe /bin/cat'' it will create the following two files:
	   -r-xr-xr-x  1 root  bin   9644 Feb 11 11:16 /bin/cat
	   -r-xr-xr-x  1 bin   bin  24576 Nov 23 13:21 /bin/cat~
       /bin/cat~ is the original file and /bin/cat is the self-uncompressing executable file.  You can remove /bin/cat~ once  you  are	sure  that
       /bin/cat works properly.

       This utility is most useful on systems with very small disks.

OPTIONS

       -d     Decompress the given executables instead of compressing them.

SEE ALSO

       bzip2(1), znew(1), zmore(1), zcmp(1), zforce(1)

CAVEATS

       The  compressed	executable  is a shell script. This may create some security holes. In particular, the compressed executable relies on the
       PATH environment variable to find gzip and some other utilities (tail, chmod, ln, sleep).

BUGS

       bzexe attempts to retain the original file attributes on the compressed executable, but you may have to fix them manually  in  some  cases,
       using chmod or chown.

																	  BZEXE(1)

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