bioawk installation issue "command not found"
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5.7 years ago
aremkho ▴ 10

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

 

bioawk Tool • 4.6k views
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3
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cross-posted on my professional email :-[

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3
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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

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0
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When i click sudo make it shows make: yacc: Command not found make: * [Makefile:50: ytab.o] Error 127

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

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5
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5.7 years ago

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

 

 

 

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

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4
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5.7 years ago
ChillarAnand ▴ 40

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

 

 

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

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12 weeks ago
Shaminur ▴ 160

Anaconda/Miniconda mignt reduce this installation process.

conda install -c bioconda bioawk
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