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