bioawk installation issue "command not found"

Question

[aremkho]

Dear All

I have a problem that we can not solved for a while in installing bioawk. I follow the general pipeline to install bioawk on ubuntu server:

• clone from git hub to the Download directory
• make

After that it is where we are stuck:

When I run the command:

mv awk book

I got error awk does not exist! When I install gawk and try mv gawk from /usr/bin to home/arsalan/download/bioawk, it works but when I cp bioawk to usr/local/bin and try to run it if fails and since gawk has already moved from /usr/bin. By typing gawk I got the error it is not installed! and typing bioawk I got error command not found!

Many thanks in advance

[Pierre Lindenbaum]

cross-posted on my professional email :-[

[Istvan Albert]

mine as well - I wish the OP put in as much effort towards fixing this very simple error as they did to track down our emails

[devhimd]

When i click sudo make it shows make: yacc: Command not found make: * [Makefile:50: ytab.o] Error 127

[ATpoint]

Please do not use the answer field for questions, use ADD REPLY.

Answer 1

[Istvan Albert]

bioawk now compiles to the executable called bioawk and not awk

it used to compile to awk and some instructions may still refer to that and instruct you to rename it

[aremkho]

Thankful of both of you! Apologize I am an newcomer in the field. Still lot to learn!

Answer 2

[ChillarAnand]

Clone bioawk repo, run make and make bioawk executable

git clone https://github.com/lh3/bioawk.git
cd bioawk
sudo make
sudo chmod +x bioawk
./bioawk

[lh3]

bioawk is standalone. It doesn't need awk/gawk preinstalled in principle, though pretty much every linux distro has awk/gawk installed by default.

Answer 3

[MSRS]

Anaconda/Miniconda mignt reduce this installation process.

conda install -c bioconda bioawk