Question: Bowtie2 Ubuntu Installation
gravatar for Nasrin
8.4 years ago by
Nasrin30 wrote:

hi all

i have downloaded bowtie2 for ubuntu 64bit. but when i try to use commands to align sequences it says that bowtie is currently not installed. im newbie in ubuntu so i do not know commands.

thanks for any advice

ubuntu bowtie • 33k views
ADD COMMENTlink modified 5 days ago by saritamaurya0 • written 8.4 years ago by Nasrin30

I have the same problem, and I didn exactly as what Sukhdeep said but still was told 'bowtie is not installed'. can anybody give a suggestion? Thanks alot

ADD REPLYlink written 8.2 years ago by adahou0

Install Instructions of bowtie2 on Ubuntu Server. It’s Super Easy! simply click on Copy button to copy the command and paste into your command line terminal using built-in APT package manager.

See below for quick step by step instructions of SSH commands, Copy/Paste to avoid miss-spelling or accidently installing a different package. Step 1 sudo apt-get update -y Step 2 sudo apt-get install -y bowtie2

ADD REPLYlink written 5 days ago by saritamaurya0
gravatar for Sukhi Singh
8.4 years ago by
Sukhi Singh10k
Sukhi Singh10k wrote:

After downloading anything, the first step is to install it.

Did you checked the manual here which says

Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with Xcode installed. Bowtie 2 can also be built on Windows using Cygwin or MinGW (MinGW recommended). If building with MinGW, first install MinGW and MSYS, the zlib library, and the pthreads library. You may also need the GnuWin32 core and other utilities to drive the build process. First, download the source package from the sourceforge site. Make sure you're getting the source package; the file downloaded should end in Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU make (usually with the command make, but sometimes with gmake) with no arguments. If building with MinGW, run make from the MSYS environment.

So, you are using Ubuntu which is a linux environment, download the package from their sourceforge or

remove the angle brackets from the following wget command

cd bowtie-0.12.8

This should install bowtie and you should be able to run /pathtofolder/bowtie-0.12.8/bowtie2 and now you can add it to PATH, so you can call it from any dir in the terminal, like just using bowtie2.

This is small snippet from my post, how to add a software to a path

Lets add the install software to path
export PATH

Check here and after that you will be able to run it from anywhere in your system.


P.S. I think you don't need multi-threading in your system, as I assume it your regular desktop, but if you want then see

To support the -p (multithreading) option, Bowtie 2 needs the pthreads library. To compile Bowtie 2 without pthreads (which disables -p), use make BOWTIE_PTHREADS=0.

ADD COMMENTlink modified 8.2 years ago • written 8.4 years ago by Sukhi Singh10k

thank you for this complete help. it helped a lot.

ADD REPLYlink written 8.4 years ago by Nasrin30
gravatar for Joe
4.5 years ago by
Joe30 wrote:

wget unzip cd bowtie-0.12.8 make

I tried this ,doesn't work. It said "make: * No targets specified and no makefile found. Stop."

I found can download bowtie package, but which documents should I download?

ADD COMMENTlink written 4.5 years ago by Joe30

Install anaconda. It will allow you to easily install most bioinformatic packages.

After installing simply type: conda install -c bioconda bowtie2 in the command line.

ADD REPLYlink written 4.5 years ago by Sinji3.0k

Installing software will now never be the same again o.O

ADD REPLYlink written 4.5 years ago by WouterDeCoster45k

Except for fact that @Joe appears to be installing bowtie1 in the original command (and then referring to bowtie2 in second half).

Unless conda install -c bioconda bowtie1 does that install ...

@Joe: bowtie1 =/= bowtie2. Which one (or both?) do you want to install?

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by GenoMax94k
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