Program runs fine from the terminal, but does not work from a shell script

Question

I am on Linux Mint.

I have program called samtools, and it is stored in a folder on my desktop. I've added path to the executable into $PATH variable. In other words my local ~/.bashrc file has a line:

export PATH="~/Desktop/samtools/samtools-1.1:$PATH"

Executable file named samtools is in this folder.

So when I try to launch it from a command line like a simple command, by just typing "samtools" it works. It also works when I type direct path to the executable in the command line.

However when I try to launch it from a shell script, it does not launch and says either No such file or directory or not found.

Actually, I am trying to use another software which uses some shell scripts to preprocess some data. The error I am getting looks like this:

Indexing...
./RD_capture//process_one_capture.sh: 17: ./RD_capture//process_one_capture.sh: samtools: not found
 Sorting...
 ./RD_capture//process_one_capture.sh: 20: ./RD_capture//process_one_capture.sh: samtools: not found
 Piling up...
./RD_capture//process_one_capture.sh: 23: ./RD_capture//process_one_capture.sh: samtools: not found

Shell code looks like this:

echo "Indexing..."
samtools index $INPUTDIR/$sample.bam
#Then we sort them
echo "Sorting..."
samtools sort $INPUTDIR/$sample.bam $TMPDIR/$sample.sorted
#Finally we pile them up
echo "Piling up..."
samtools mpileup $TMPDIR/$sample.sorted.bam | cut -f 1-4 > $OUTPUT/$(basename $sample .bam).pile

Can anyone help me to solve this problem?

Answer 1

It looks like Linux is not able to find samtools .

To solve this use: Declare this in the beginning (change pwd with the path that leads to executable from pwd )

export set CURRENT_DIR=`pwd`

and while calling samtools use

$CURRENT_DIR/samtools

Note 1: you are responsible to tell the exact path to shell script as shell scripts execute from /usr/bin/sh . try echoing the path on the console with the command, if this does not help, as follows:

echo `pwd`

Note 2: the use of back quote above that is located on left hand side top corner of your keyboard.

Note 3: the export set is used to store global variables in a shell script so that commands that appear after this command can use this variable and update it when ever required.