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Newbie wanting help with a script

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# 1  
Old 09-18-2011
Newbie wanting help with a script
Hi

I am new to scripting and having trouble with an assignment. I have written this script:

Code:
#!/bin/bash

PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin

printf "\nWhat is the name of the input file?  "
read INPUT_FILE

if test ! -f ./$INPUT_FILE ; then
  printf "\nNo matching file name!!!  Aborting!!!\n\n"
  exit 192
fi

clustalw -align -INFILE=$INPUT_FILE -TYPE=DNA -OUTFILE=$INPUT_FILE_clustal.output -OUTPUT=PHYLIP

collapse1.5 $INPUT_FILE_clustal.output > $INPUT_FILE_collapse.output

seqret  -nofeature -sequence $INPUT_FILE_collapse.output -sformat1 phylip -snucleotide1 -nofirstonly -outseq $INPUT_FILE.nexus -osformat nexusnon -auto

rm -f *.output


But I get this error message in the terminal:


Code:
Foyn@Havard-Foyns-MacBook-Air:~/Desktop/Foyn_Miniproject_2_Part_1$ Miniproject_2_script 

What is the name of the input file?  Part_2_Seq.fasta
/Users/Foyn/UNIX_progs/bin/Miniproject_2_script: line 20: clustalw: command not found
/Users/Foyn/UNIX_progs/bin/Miniproject_2_script: line 24: collapse1.5: command not found
/Users/Foyn/UNIX_progs/bin/Miniproject_2_script: line 28: seqret: command not found


When I run the individual commands in the terminal on the other hand it seems to be working.

Is there anyone that knows what the problem is??
Last edited by pludi; 09-18-2011 at 06:41 PM..
# 2  
Old 09-18-2011
It is your PATH variable...why dont you copy the PATH from the terminal into the script instead of initializing it to dirs that dont contain those commands...clustal seqret collapse1.5
This User Gave Thanks to shamrock For This Post:
foyn
# 3  
Old 09-18-2011
Thank you. Have done that now and the first part is now working (clustalw), but now I get the following error:


PHYLIP-Alignment file created [.output]


ERROR: the input file does not seem to be a valid Phylip file
collapse1.5(1635) malloc: *** mmap(size=140737488355328) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug


Seems like the output file is not named correctly so collapse1.5 don't find the input. Is there something wrong with my INPUT_FILE variable?

---------- Post updated at 09:11 PM ---------- Previous update was at 09:07 PM ----------

Fixed it
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