TopHat Installation problem version 1.1.2

[waterboy]

Dear Friends,

I am Shilp Purohit, and I am currently working with ABI SOLiD 3 plus sequencer. I am trying to install TopHat 1.1.2 (BETA) on my local machine. The "Getting started" manual suggests that I need to run following commands:

./configure
make
make install

However, the unzipped tar package doesn't have these files to execute, i.e. configure, make file and install file.

On the other hand, I unzipped tar package of TopHat version 1.1.0 and it worked absolutely fine and installed correctly just because the package consisted of these three files. But this version doesn't support the colorspace format of SOLiD.

Can anyone please suggest me as to how to install version 1.1.2? Any suggestions will be highly appreciated.

I am looking forward to having a reply soon.

Thanking you.

[lshen]

Are you working on the source code?

http://tophat.cbcb.umd.edu/downloads/tophat-1.1.2.tar.gz

[masylichu]

The Tophat depend on samtools, so you first should install samtools correctly.

here is the manual about samtools' install.

http://cufflinks.cbcb.umd.edu/tutorial.html

after this, choose your directory, follow the author's manual . OK !

Dear Friends,

I am Shilp Purohit, and I am currently working with ABI SOLiD 3 plus sequencer. I am trying to install TopHat 1.1.2 (BETA) on my local machine. The "Getting started" manual suggests that I need to run following commands:

./configure
make
make install

However, the unzipped tar package doesn't have these files to execute, i.e. configure, make file and install file.

On the other hand, I unzipped tar package of TopHat version 1.1.0 and it worked absolutely fine and installed correctly just because the package consisted of these three files. But this version doesn't support the colorspace format of SOLiD.

Can anyone please suggest me as to how to install version 1.1.2? Any suggestions will be highly appreciated.

I am looking forward to having a reply soon.

Thanking you.

[Daehwan]

Please note it is also explained in README.

[waterboy]

Dear Folks..!

Eventually I came to know that I downloaded the wrong version myself, and everything works fine now.. I've got results on my test data too and now I've started my transcriptome run on the data so I'll have results with my by tomorrow morning..

Thank you very much for your replies..

and do drop me an email if anyone from this community needs any help with installation.. I'll be happy to help..

Cheers..
Water Boy