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seqtk: command not found

Hi, Im using Git bash in my Windows computer, I want to install seqtk, I followed this path

git clone https://github.com/lh3/seqtk.git cd seqtk

Then when I invoke seqtk appear a message "seqtk: command not found". How can I install step by step seqtk in git bash in windows?

Thanks a lot

Adriana

rna-seq
• 8,173 views • link
updated by cpad0112 cpad0112 • written by adriana.gallego.02 • adriana.gallego.02

1 answer

you should compile the program: Follow the instructions on page (https://github.com/lh3/seqtk)

cd seqtk; make
• 0 views • link
written by cpad0112 cpad0112

adriana.gallego.02 : If you don't have gcc/make/zlib installed then you would need to get those first.

$ sudo apt-get install gcc make
$ sudo apt-get install  zlib1g zlib1g-dev
• 0 views • link
written by GenoMax GenoMax

Are you using windows 10? Then install bash on windows rather than using git bash. Simple way to do this is windows key --> bash --> Should open a new command prompt window. Will ask you if you want to install Ubuntu on windows. Follow the prompts. Create a new unix username/password. This is separate from your windows username/password.

It should take less than 10 min depending on your internet speed to download/install Ubuntu/bash.

• 0 views • link
written by GenoMax GenoMax

" Git bash " is a msys shell included in "Git for Windows", and is a slimmed-down version of Cygwin (an old version at that), whose only purpose is to provide enough of a POSIX layer to run a bash.

• 0 views • link
written by GenoMax GenoMax

Hi! I have a similar issue. I installed seqtk using following commands:

git clone https://github.com/lh3/seqtk.git; cd seqtk; make

then it gave me error: "seqtk: command not found"

So now I used your commands: sudo apt-get install gcc make but it tells me "apt-get: command not found"

What should I do?

• 1 views • link
written by writetoroopali • writetoroopali

This is the error when I follow the instructions using my Git bash in windows plattform

$ cd seqtk; make bash: make: command not found

• 0 views • link
written by adriana.gallego.02 • adriana.gallego.02

See my comment above.

• 0 views • link
written by GenoMax GenoMax

I am not sure if you can compile seqtk on windows without compilers installed (like make etc). Btw, which version of windows are you using? One of the recent versions of windows allows user to run ubuntu along with windows 10.

• 0 views • link
written by cpad0112 cpad0112

Hi, I have windows 10 and I have not been able to install seqtk in git bash. Could some body help me? It looks sudo is not recognized also.

Thanks Adriana

• 0 views • link
written by adriana.gallego.02 • adriana.gallego.02

You can't use git bash as a replacement for a real bash shell. So that is not going to work for this.

Please follow the directions I gave in the post above to install Ubuntu for Win 10 and then follow the rest of the directions.

Otherwise tell us what you are trying to do with seqtk and we may be able to suggest alternative java programs that may work natively on windows.

• 0 views • link
written by GenoMax GenoMax

Hi genomax. Is this the only way? Is it not possible to use MinGW/msys to compile it on windows?

Because I've compiled the library dependency zlib but I'm still struggling to compile seqtk. Wondering if I'm barking up the wrong tree.

Apologies if this is very naive.

• 0 views • link
written by a.b.g • a.b.g

It may be possible to use MinGW but the hassle may not be worth it.

What do you plan to use seqtk for? There may be an alternate program we can suggest that will work on Windows.

• 0 views • link
written by GenoMax GenoMax

Thanks genomax. I needed it for pulling out fastq sequences from multiple files based on a list of sequence IDs. I actually ended up following your advice above and installing the Ubuntu subsystem. It works a charm (but wouldn't mind knowing about alternatives).

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written by a.b.g • a.b.g

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