Linux – Executable Launches from Terminal but Not from Shell Script

I have downloaded some software (called samtools) and it is stored in a folder on my desktop.
Then I've added the path to the executable into the PATH environment variable.
In other words my ~/.bashrc file has the following line:

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

The executable file named samtools is in this folder.

When I try to launch it from the command line by simply typing samtools, it works. It also works when I use the full path to the executable.

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

Can anyone help me to solve this problem?

EDIT:
As some people requested.

The exact error message is:

Realigning using Bowtie2...
./RP_capture//realign/filter_long_inserts.sh: 29: ./RP_capture//realign/filter_long_inserts.sh: samtools: not found
./RP_capture//realign/filter_long_inserts.sh: 29: ./RP_capture//realign/filter_long_inserts.sh: samtools: not found
Could not locate a Bowtie index corresponding to basename "./aux/chr1.fa"

I have also added echo $PATH to my script and the output seems correct. Path to samtools is there.

this is example of one of many calls to samtools from the script.

samtools index $OUTPUT/realignments/$file.abnormal.realign.bowtie.bam

I have actually managed to solve the problem using

export set SAMTOOLS_DIR="/home/laba/Desktop/samtools/samtools-1.1"

within a script and then calling samtools like this:

$SAMTOOLS_DIR/samtools [parameters]

Strangely enough, another binary script calls works with just explicitly providing path to the executable. Without having to use set.