Help installing/running TopHat and Cufflinks

[ifyouseqamy]

I need to use TopHat and Cufflinks, for which I must obtain Bowtie2, Boost, and SAM tools. I have managed to successfully install Bowtie2, but I've had no such luck with the other two. I'm using a Mac (OS X version 10.7.4), and I'm not the administrator (don't think that's the issue, given the error messages I get). I was wondering if I could get some help.

I have downloaded the two files (boost_1_52_0.tar.bz2 and tabix-0.2.6.tar.bz2 from here and here, respectively) as linked in the TopHat website. They are now in my desktop, i.e. /Users/ifyouseqamy/Desktop/boost_1_52_0.tar.bz2 and /Users/ifyouseqamy/Desktop/tabix-0.2.6.tar.bz2).

On Terminal, I've accessed my institution's server via SSH (where I'd be using TopHat and Cufflinks) and inserted the following in the command line, as instructed in the Boost website:

tar --bzip2 -xf /Users/ifyouseqamy/Desktop/boost_1_52_0.tar.bz2/

This is what I get:

tar: /Users/ifyouseqamy/Desktop/boost_1_52_0.tar.bz2/: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors

I get the same error messages when I try the SAM tools .tar.bz2 file.

Then I thought I'd use this to get the .tar file first:

bzip2 -d /Users/ifyouseqamy/Desktop/boost_1_52_0.tar.bz2/

Followed by:

tar -xvf /Users/ifyouseqamy/Desktop/boost_1_52_0.tar.bz2/

But I get this after I attempt the first command:

bzip2: Can't open input file /Users/job2052/Desktop/boost_1_52_0.tar.bz2: No such file or directory.

So, it seems as though there's "No such file in directory"! Except there is. I have no idea what's going on. Help, please!

[mike.t]

Try this:

tar -xjf /Users/ifyouseqamy/Desktop/boost_1_52_0.tar.bz2

Don't put the trailing slash / at the end of a file name.

I have tophat and cufflinks running on a MacPro box and I don't remember having to install boost. Are you sure you need it? Are you installing the precompiled binaries of tophat and cufflinks?

[ifyouseqamy]

Thanks, Mike!