Shell script not running command not found

Question

I am very  very new to UNIX programming  running on MacOSX Mountain Lion via Terminal   I ve been learning the basics from a bioinformatics and molecular methods course  we ve had two classes  where we will eventually be using perl and python for data management purposes   Anyway  we have been tasked with writing a shell script to take data from a group of files and write it to a new file in a format that can be read by a specific program  Migrate-N     I have gotten a number of functions to do exactly what I need independently when I type them into the command line  but when I put them all together in a script and try to run it I get an error  Here are the details  I apologize for the length        bin bash  grep -f Samples NFCup txt locus1 fasta  gt  locus1 NFCup txt grep -f Samples NFCup txt locus2 fasta  gt  locus2 NFCup txt grep -f Samples NFCup txt locus3 fasta  gt  locus3 NFCup txt grep -f Samples NFCup txt locus4 fasta  gt  locus4 NFCup txt grep -f Samples NFCup txt locus5 fasta  gt  locus5 NFCup txt grep -f Samples Salmon txt locus1 fasta  gt  locus1 Salmon txt grep -f Samples Salmon txt locus2 fasta  gt  locus2 Salmon txt grep -f Samples Salmon txt locus3 fasta  gt  locus3 Salmon txt grep -f Samples Salmon txt locus4 fasta  gt  locus4 Salmon txt grep -f Samples Salmon txt locus5 fasta  gt  locus5 Salmon txt grep -f Samples Cascades txt locus1 fasta  gt  locus1 Cascades txt grep -f Samples Cascades txt locus2 fasta  gt  locus2 Cascades txt grep -f Samples Cascades txt locus3 fasta  gt  locus3 Cascades txt grep -f Samples Cascades txt locus4 fasta  gt  locus4 Cascades txt grep -f Samples Cascades txt locus5 fasta  gt  locus5 Cascades txt  echo 3 5 Salex melanopsis  gt  Smelanopsis mig echo 656 708 847 1159 779  gt  gt  Smelanopsis mig echo 154 124 120 74 126 NFCup  gt  gt  Smelanopsis mig cat locus1 NFCup txt locus2 NFCup txt locus3 NFCup txt locus4 NFCup txt locus5 NFCup txt  gt  gt  Smelanopsis mig echo 32 30 30 18 38 Salmon River  gt  gt  Smelanopsis mig cat locus1 Salmon txt locus2 Salmon txt locus3 Salmon txt locus4 Salmon txt locus5 Salmon txt  gt  gt  Smelanopsis mig echo 56 52 24 29 48 Cascades  gt  gt  Smelanopsis mig cat locus1 Cascades txt locus2 Cascades txt locus3 Cascades txt locus4 Cascades txt locus5 Cascades txt  gt  gt  Smelanopsis mig   The series of greps are just pulling out DNA sequence data for each site for each locus into new text files  The Samples   txt files have the sample ID numbers for a site  the  fasta files have the sequence information organized by sample ID  the grepping works just fine in command line if I run it individually    The second group of code creates the actual new file I need to end up with  that ends in  mig  The echo lines are data about counts  basepairs per locus  populations in the analysis  samples per site  etc   that the program needs information on  The cat lines are to mash together the locus by site data created by all the grepping below the site-specific information dictated in the echo line  You no doubt get the picture   For creating the shell script I ve been starting in Excel so I can easily copy-paste autofill cells  saving as tab-delimited text  then opening that text file in TextWrangler to remove the tabs before saving as a  sh file  Line breaks  Unix  LF  and Encoding  Unicode  UTF-8   in the same directory as all the files used in the script  I ve tried using chmod  x FILENAME sh and chmod u x FILENAME sh to try to make sure it is executable  but to no avail  Even if I cut the script down to just a single grep line  with the     bin bash first line  I can t get it to work   The process only takes a moment when I type it directly into the command line as none of these files are larger than 160KB and some are significantly smaller  This is what I type in and what I get when I try to run the file  HW is the correct directory   localhost HW Mirel  MigrateNshell sh -bash  MigrateNshell sh  command not found   I ve been at this impass for two days now  so any input would be greatly appreciated  Thanks

User · Answer

For security reasons  the shell will not search the current directory  by default  for an executable  You have to be specific  and tell bash that your script is in the current directory           MigrateNshell sh

User · Answer

Also try to dos2unix the shell script  because sometimes it has Windows line endings and the shell does not recognize it     dos2unix MigrateNshell sh   This helps sometimes

User · Answer

Change the first line to the following as pointed out by Marc B     bin bash    Then mark the script as executable and execute it from the command line  chmod  x MigrateNshell sh   MigrateNshell sh   or simply execute bash from the command line passing in your script as a parameter   bin bash MigrateNshell sh

User · Answer

Unix has a variable called PATH that is a list of directories where to find commands     echo  PATH  usr local bin  usr bin  bin  usr sbin  sbin  usr local bin  Users david bin   If I type a command foo at the command line  my shell will first see if there s an executable command  usr local bin foo  If there is  it will execute  usr local bin foo  If not  it will see if there s an executable command  usr bin foo and if not there  it will look to see if  bin foo exists  etc  until it gets to  Users david bin foo   If it can t find a command foo in any of those directories  it tell me command not found   There are several ways I can handle this issue    Use the commandbash foo since foo is a shell script  Include the directory name  when you eecute the command like  Users david foo or  PWD foo or just plain   foo  Change your  PATH variable to add the directory that contains your commands to the PATH    You can modify  HOME  bash profile or  HOME  profile if  bash profile doesn t exist  I did that to add in  usr local bin which I placed first in my path  This way  I can override the standard commands that are in the OS  For example  I have Ant 1 9 1  but the Mac came with Ant 1 8 4  I put my ant command in  usr local bin  so my version of antwill execute first  I also added  HOME bin to the end of the PATH for my own commands  If I had a file like the one you want to execute  I ll place it in  HOME bin to execute it

User · Answer

There have been a few good comments about adding the shebang line to the beginning of the script   I d like to add a recommendation to use the env command as well  for additional portability   While    bin bash may be the correct location on your system  that s not universal   Additionally  that may not be the user s preferred bash      usr bin env bash will select the first bash found in the path

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Add below lines in your  profile path  PATH  PATH  HOME bin  Dir where script exists  export PATH   Now your script should work without     Raj Dagla

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I m new to shell scripting too  but I had this same issue  Make sure at the end of your script you have a blank line  Otherwise it won t work

User · Answer

bin bash    ---   remove the indicated space  The shebang should be     bin bash

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Make sure you are not using  PATH  as a variable  which will override the existing PATH for environment variables

User · Answer

First   chmod 777   MigrateNshell sh   Then     MigrateNshell sh   Or  add your program to a directory recognized in your  PATH variable   Example  Path Variable Example Which will then allow you to call your program without

User · Answer

Also make sure  bin bash is the proper location for bash      if you took that line from an example somewhere it may not match your particular server  If you are specifying an invalid location for bash you re going to have a problem

User · Answer

Try chmod u x MigrateNshell sh

[bash] Shell script not running, command not found

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