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linux - Executable lauches if called directly from terminal, but does not work when called 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.



Answer



Setting directory variable like this:


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

And then calling the exacutable from the script like this:


$SAMTOOLS_DIR/samtools [parameters]

solves the problem


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