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Old 02-06-2013, 11:48 AM   #1
whp09
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Default Bowtie2 installation

So, I am a complete beginner to both sequencing and linux (and thus the terminal as well.) I have been beating myself up for hours attempting to install bowtie2, and I know there is a simple answer right in front of my face.

Using 'sudo apt-get install bowtie' installs bowtie1, and replacing it with bowtie2 will not install because it says the program doesn't exist.

If I download the linuxx64_84 version of bowtie2-2.0.6, I can use the terminal to change the directory to the bowtie2-2.0.6 folder (after unzipping it) but then I am lost. I have heard to try to use ./configure and make.

./configure tells me - configure: command not found

make tells me- ***No targets specified or no makefiles found. Stop.

Any help would be much appreciated!
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Old 02-06-2013, 12:04 PM   #2
GenoMax
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Looks like you will need to apt-get the "build-essential" package.
That should get you the stuff needed to configure/compile/make programs.

http://packages.debian.org/sid/build-essential
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Old 02-06-2013, 05:07 PM   #3
whp09
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Quote:
Originally Posted by GenoMax View Post
Looks like you will need to apt-get the "build-essential" package.
That should get you the stuff needed to configure/compile/make programs.

http://packages.debian.org/sid/build-essential
I tried this:

billy@ubuntu:~$ sudo apt-get install build-essential
Reading package lists... Done
Building dependency tree
Reading state information... Done
build-essential is already the newest version.

So does that mean that I already have this?
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Old 02-06-2013, 06:15 PM   #4
whp09
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Here is the screen I look at after I unzip the downloaded file. I also opened a "README" document located in the "doc" folder shown on the screen.
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Old 02-07-2013, 03:12 AM   #5
GenoMax
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Based on the screenshot you posted I think you have already downloaded the pre-compiled version of bowtie2 that is ready for use (Did the file you downloaded have the word "source" in the file name or was it this file "bowtie2-2.0.6-linux-x86_64.zip"?). All you may need to do is to add bowtie2 directory (currently the folder is sitting on your desktop may want to move somewhere else) to your PATH variable: http://bowtie-bio.sourceforge.net/bo...adding-to-path

On a different note:

Bowtie2 appears to be available in the quantal repositories: http://ubuntuguide.org/wiki/Ubuntu_Quantal_Repositories You may need to add that source to get the bowtie2 package: http://packages.ubuntu.com/quantal/science/bowtie2
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Old 02-09-2013, 01:44 PM   #6
whp09
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Quote:
Originally Posted by GenoMax View Post
Based on the screenshot you posted I think you have already downloaded the pre-compiled version of bowtie2 that is ready for use (Did the file you downloaded have the word "source" in the file name or was it this file "bowtie2-2.0.6-linux-x86_64.zip"?). All you may need to do is to add bowtie2 directory (currently the folder is sitting on your desktop may want to move somewhere else) to your PATH variable: http://bowtie-bio.sourceforge.net/bo...adding-to-path

On a different note:

Bowtie2 appears to be available in the quantal repositories: http://ubuntuguide.org/wiki/Ubuntu_Quantal_Repositories You may need to add that source to get the bowtie2 package: http://packages.ubuntu.com/quantal/science/bowtie2
You're correct, I did not download the source one. I will try adding it to my PATH variable (thanks for the link, because I have never done that). Told you I was a noob!

I will let you know how it goes, and thank you.

Last edited by whp09; 02-09-2013 at 01:44 PM. Reason: spelling
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Old 02-09-2013, 03:39 PM   #7
feseha
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Default bowtie

Frome 1 newbie 2 1-other

You are on Linux you have two choices:
1: download the precompiled version in which case all you have to do
is to change the permission levels to executable (755) and place them
in an a directory in your path or add the folder to your path and you are set.
./configure or make are unnecessary as the prograns are precompiled ...
To be specific, these are the scripts you need for bowtie related work.

bowtie2
bowtie2-align
bowtie2-align-debug
bowtie2-build
bowtie2-build-debug
bowtie2-inspect
bowtie2-inspect-debug
bowtie2sam.pl
and all the scripts in the scripts file have to be made executable and
made visible to your PATH!

For example, I put these executables and associated scripts in my /opt.bioInfoBin/ directory
and they are working fine ... out of the box - the only change, as mentioned above making them
executable( chmod 755 ...)


2. if you want to build from source get the source bundle: bowtie2-2.0.0-beta6-source.zip
unzip it and descend into the unzipped folder and build using GNU make ... that will build
the boutie tools ... Below is actually the actual instruction lifted from the installation
guideline that is available as "manual.html" file in the doc directory ...


... First, download the source package from the sourceforge site. Make sure you're getting the source package; the file downloaded should end in -source.zip. 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.

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.
Adding to PATH

By adding your new Bowtie 2 directory to your PATH environment variable, you ensure that whenever you run bowtie2, bowtie2-build or bowtie2-inspect from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system's instructions for adding the directory to your PATH.



I hope this helps
Feseha
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Old 02-10-2013, 05:23 PM   #8
ARopski
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Default Installed bowtie2, can't run paired-end alignments

After installation of bowtie and bowtie2 with msys, I successfully ran the 1st and 3rd trials for the lambda phage example, as explained in the user manual. However, the 2nd part for paired-ends results in an error stating that 'bowtie2-align has stopped working'. Looks like a windows issue.

I have been able to run paired-end alignments in Bowtie, and in trying to use the same dataset with Bowtie2, I get the same error mentioned above.

I've checked my PATH assignments, but maybe missed something else during install?
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