unable to call "samtools"

[ehjChun]

Hello,

I am trying to run fragCounter to generate one of the required input files for JaBbA, i.e. coverage.txt. I was able to install it successfully (I think), and tried to run it on your test data: > ./bin/fragCounter-master/frag -b ./bin/fragCounter-master/inst/extdata/chr21.bam -d ./bin/fragCounter-master/inst/extdata/gcMAP21/ -w 200

One of the output messages was the following, which indicates that it cannot call the samtools:

Calling samtools view  -f 0x02 -F 0x10 ./bin/fragCounter-master/inst/extdata/chr21.bam -q 1 | cut -f "3,4,9"
sh: samtools: command not found

My samtools has indeed been installed, and is aliased in my bashrc file as below:

> which samtools
alias samtools='/user/bin/linux-x86_64/samtools-0.1.17/samtools'
    /user/bin/linux-x86_64/samtools-0.1.17/samtools

Would you be able to tell me what I need to do (e.g. modify in your code) in order for fragCounter to recognize my samtools executable?

Thanks very much for your help.

[mskilab]

I don't think aliases get expanded in non interactive shell sessions

You should instead put the samtools executable in the PATH var

On Mon, Aug 23, 2021 at 8:12 PM ehjChun @.***> wrote:

Hello,

I am trying to run fragCounter to generate one of the required input files for JaBbA, i.e. coverage.txt. I was able to install it successfully (I think), and tried to run it on your test data:

./bin/fragCounter-master/frag -b ./bin/fragCounter-master/inst/extdata/chr21.bam -d ./bin/fragCounter-master/inst/extdata/gcMAP21/ -w 200

One of the output messages was the following, which indicates that it cannot call the samtools:

Calling samtools view -f 0x02 -F 0x10 ./bin/fragCounter-master/inst/extdata/chr21.bam -q 1 | cut -f "3,4,9" sh: samtools: command not found

My samtools has indeed been installed, and is aliased in my bashrc file as below:

which samtools alias samtools='/user/bin/linux-x86_64/samtools-0.1.17/samtools' /user/bin/linux-x86_64/samtools-0.1.17/samtools

Would you be able to tell me what I need to do (e.g. modify in your code) in order for fragCounter to recognize my samtools executable?

Thanks very much for your help.

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[ehjChun]

Ah, that indeed solved the problem - Thank you!