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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC73JELKZYDSUXXG6OVMUETT6LPYVANCNFSM5CVWCSTQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[ehjChun]

Ah, that indeed solved the problem - Thank you!