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 > locus1.NFCup.txt grep -f Samples.NFCup.txt locus2.fasta > locus2.NFCup.txt grep -f Samples.NFCup.txt locus3.fasta > locus3.NFCup.txt grep -f Samples.NFCup.txt locus4.fasta > locus4.NFCup.txt grep -f Samples.NFCup.txt locus5.fasta > locus5.NFCup.txt grep -f Samples.Salmon.txt locus1.fasta > locus1.Salmon.txt grep -f Samples.Salmon.txt locus2.fasta > locus2.Salmon.txt grep -f Samples.Salmon.txt locus3.fasta > locus3.Salmon.txt grep -f Samples.Salmon.txt locus4.fasta > locus4.Salmon.txt grep -f Samples.Salmon.txt locus5.fasta > locus5.Salmon.txt grep -f Samples.Cascades.txt locus1.fasta > locus1.Cascades.txt grep -f Samples.Cascades.txt locus2.fasta > locus2.Cascades.txt grep -f Samples.Cascades.txt locus3.fasta > locus3.Cascades.txt grep -f Samples.Cascades.txt locus4.fasta > locus4.Cascades.txt grep -f Samples.Cascades.txt locus5.fasta > locus5.Cascades.txt  echo 3 5 Salex_melanopsis > Smelanopsis.mig echo 656 708 847 1159 779 >> Smelanopsis.mig echo 154 124 120 74 126 NFCup >> Smelanopsis.mig cat locus1.NFCup.txt locus2.NFCup.txt locus3.NFCup.txt locus4.NFCup.txt locus5.NFCup.txt >> Smelanopsis.mig echo 32 30 30 18 38 Salmon River >> Smelanopsis.mig cat locus1.Salmon.txt locus2.Salmon.txt locus3.Salmon.txt locus4.Salmon.txt locus5.Salmon.txt >> Smelanopsis.mig echo 56 52 24 29 48 Cascades >> Smelanopsis.mig cat locus1.Cascades.txt locus2.Cascades.txt locus3.Cascades.txt locus4.Cascades.txt locus5.Cascades.txt >> 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!!

Answer 1

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