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Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

Tophat

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with either the qsh or qrsh command.

The latest version of tophat (currently 2.1.0) is made available with the command:

module apps/gcc/4.8.2/tophat

Alternatively, you can load a specific version with

module load apps/gcc/4.8.2/tophat/2.1.0

This command makes the tophat binary available to your session.

Installation notes

Tophat 2.1.0 was installed using gcc 4.8.2. Installs were attempted using gcc 5.2 and gcc 4.4.7 but both failed (see this issue on github )

This install has dependencies on the following

Install details

module load compilers/gcc/4.8.2
module load libs/gcc/4.8.2/boost/1.58

mkdir -p /usr/local/packages6/apps/gcc/4.8.2/tophat/2.1.0

tar -xvzf ./tophat-2.1.0.tar.gz
cd tophat-2.1.0
./configure --with-boost=/usr/local/packages6/libs/gcc/4.8.2/boost/1.58.0/ --prefix=/usr/local/packages6/apps/gcc/4.8.2/tophat/2.1.0

Configuration results

-- tophat 2.1.0 Configuration Results --
C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/packages6/libs/gcc/4.8.2/boost/1.58.0//include -I./SeqAn-1.3
Linker flags:        -L./samtools-0.1.18 -L/usr/local/packages6/libs/gcc/4.8.2/boost/1.58.0//lib
BOOST libraries:     -lboost_thread -lboost_system
GCC version:         gcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15)
Host System type:    x86_64-unknown-linux-gnu
Install prefix:      /usr/local/packages6/apps/gcc/4.8.2/tophat/2.1.0
Install eprefix:     ${prefix}

Built with

make
make install

Testing

A test script was executed based on the documentation on the tophat website (retrieved 29th October 2015). It only proves that the code can run without error, not that the result is correct.

Modulefile

  • The module file is on the system at /usr/local/modulefiles/apps/gcc/4.8.2/tophat/2.1.0

  • The module file is on github