Tophat Installation On Ubuntu 11.10 Server

Question

[U]

Hi,

I am very new to Ubuntu and please bear with me if I present a very layman's version of explanation.

My OS: Ubuntu 11.10 server, 64bit version

I need to use three tools samtools, bowtie and tophat. However tophat is dependent upon samtools and bowtie. The dependency factor is - to ascertain where exactly the path to the above two tools (samtools and bowtie) are located.

Now, I can install samtools and bowtie by sudo apt-get install

1. However I don't know exactly where the library paths exists for samtools or bowtie
2. According to the tophat installation notes, I am to extract the tool from compressed file, change dir into this file and ./configure; BUT I don't see the ./configure script in the extracted directory

SAMTOOLS and BOWTIE

• http://samtools.sourceforge.net/
• http://bowtie-bio.sourceforge.net/index.shtml

TOPHAT:

• http://tophat.cbcb.umd.edu/tutorial.html
• Installation Of Tophat -1.1.4

Many thanks

Uma

[Rm]

type "which samtools" or bowtie to know the location

[U]

Thank you. I will try re-installation.

[U]

For some reason this method doesnt work. But previous I had working for mac and ubuntu 9.10

[U]

Thanks for the previous comments, I will have a go at this again.

[Casey Bergman]

Hi Uma, comment like these should be added to individual answers

[U]

Just as an update, with the configure script.. the error is to declare the bam-root

checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in [?]. See http://randspringer.de/bam for more documentation.

[Casey Bergman]

Hi Uma, these updates should go as edits in the original question.

Answer 1

[Matt Shirley]

To answer your two questions, I'll break this in to two parts:

1. To find the binary (program) that you installed with apt (Ubuntu's package manager), you can simply type "$ type {target}", with {target} being for instance samtools. This will result in something that tells you "{target} is $path" or, for my installation of samtools:

   $ type samtools samtools is /usr/local/bin/samtools

This should work on any linux distribution where you are using the bash shell.

1. I downloaded the TopHat source code, and there is indeed a "configure" script in the archive. Is it possible that you have downloaded the linux binaries instead? Here is the link to the source code archive: TopHat source.

If you want to download the binaries (which I suspect you have, since the README file in the binary archive contains directions for compiling from source) instead of compiling the source code, you can just copy the contents of the archive to a folder in the user's PATH. To do this, you can do the following:

1. tar -xvzf tophat-{version}.Linux_x86_64.tar.gz
2. cd tophat-{version}.Linux_x86_64
3. echo $PATH # this will give you a list of directories are searched when you specify a program name to run
4. Choose a directory from the PATH to copy the files to. I would suggest /usr/local/bin. Then issue "$ find . -perm /o=x -exec cp {} /usr/local/bin ;". This will find the executable binaries in this folder, skipping the documentation, and copy to /usr/local/bin.

I hope this helps!

[martinkara7]

Hello, I am using Linux_x86_64 tophat. Can I ask question about samtools and boost. Do I still need these with linux version and if so is the installation for these the way it say on the tophat website http://tophat.cbcb.umd.edu/tutorial.shtml ? Thank you very much for the answer above it was very helpful to me too.

[Matt Shirley]

You only need to install Boost and Samtools if you want to build tophat from the source code. If you download the precompiled binary you will not need either one.

[martinkara7]

got it, thanks,

[martinkara7]

Hello again, another question. I am now installing cufflinks. I downloaded boost as it say but I cant find bjam to download. I know silly question, sorry but I looked all over boost website and googled it, but no luck. Maybe its early morning and i just keep missing it. So where is bjam build engine download? or is it part of something else? Thanks

[Matt Shirley]

You don't need to install anything else. Just follow the instructions in easy build and install. It's not clear to me that you really need the boost libraries. Why are you building cufflinks from source? If you are using a 64bit linux machine why not just download the binary distribution? Take some time and read about the process of compiling code and understand why and what it is before you blindly rush in to it. Especially if the software you are compiling does not have built in functional testing.

Answer 2

[Farhat]

The following should work on the command line

tar xvzf tophat-1.4.0.tar.gz

Use the appropriate file name above if that is not correct

cd tophat-1.4.0/

Change to the directory (may be different depending on version number)

Now build the package:

./configure --prefix=/usr/local/bin

After the configure script finishes successfully, build the Tophat package:

make

Finally, install TopHat:

sudo make install

[bioinformaticssrm2011]

There is no such file or directory, while using command ./config

Answer 3

[Casey Bergman]

The Bio-linux team has been actively packaging NGS tools, including SAMtools, Bowtie, Tophat and Cufflinks, for easy installation on Ubuntu systems: https://launchpad.net/~nebc/+archive/galaxy

[Steve Moss]

Only thing with some of the BioLinux tools, is that they aren't always the latest versions, however, I think this is probably the easiest way to do it :) +1