Question: bioawk installation issue "command not found"
0
gravatar for aremkho
2.8 years ago by
aremkho0
United States
aremkho0 wrote:

Dear All

I have a problem that we can not solved for a while in installing bio awk.

I follow the general pipe line 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

 

tool bioawk • 2.1k views
ADD COMMENTlink modified 2.8 years ago by ChillarAnand30 • written 2.8 years ago by aremkho0
1

cross-posted on my professional email :-[

ADD REPLYlink written 2.8 years ago by Pierre Lindenbaum108k
1

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

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 77k
5
gravatar for Istvan Albert
2.8 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

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

 

 

 

ADD COMMENTlink written 2.8 years ago by Istvan Albert ♦♦ 77k

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

ADD REPLYlink written 2.8 years ago by aremkho0
3
gravatar for ChillarAnand
2.8 years ago by
ChillarAnand30
India
ChillarAnand30 wrote:

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

 

 

ADD COMMENTlink modified 19 months ago • written 2.8 years ago by ChillarAnand30
1

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

ADD REPLYlink written 2.8 years ago by lh330k
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