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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 using sudo apt-get install however

  • I dont know exactly where the library paths exists for samtools or bowtie
  • According to the tophat installation notes, I am to extract the tool from compressed file, change dir into this file and ./configure; BUT I dont see the ./configure script in the extracted directory

Samtools and Bowtie and Tophat are found on their sites, this is the installation method I am trying to follow.

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To find out where the libraries are installed, you could try dpkg -L samtools and the same for bowtie

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