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bitseq

Transcript isoform level expression and differential expression estimation for RNA-seq

Interactive Usage

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

module load apps/gcc/5.2/bitseq

Alternatively, you can load a specific version with

module load apps/gcc/5.2/bitseq/0.7.5

This command adds the BitSeq binaries to your PATH.

Documentation

Documentation is available online http://bitseq.github.io/howto/index

Installation notes

BitSeq was installed using gcc 5.2

module load compilers/gcc/5.2
tar -xvzf ./BitSeq-0.7.5.tar.gz
cd BitSeq-0.7.5

make
cd ..
mkdir -p /usr/local/packages6/apps/gcc/5.2/bitseq
mv ./BitSeq-0.7.5 /usr/local/packages6/apps/gcc/5.2/bitseq/

Testing

No test suite was found.

Modulefile

  • The module file is on the system at /usr/local/modulefiles/apps/gcc/5.2/bitseq/0.7.5. It’s contents

    #%Module1.0#####################################################################
    ##
    ## bitseq 0.7.5 modulefile
    ##
    
    ## Module file logging
    source /usr/local/etc/module_logging.tcl
    ##
    
    module load compilers/gcc/5.2
    
    
    proc ModulesHelp { } {
            puts stderr "Makes bitseq 0.7.5 available"
    }
    
    set version 0.7.5
    set BITSEQ_DIR /usr/local/packages6/apps/gcc/5.2/bitseq/BitSeq-$version
    
    module-whatis   "Makes bitseq 0.7.5 available"
    
    prepend-path PATH $BITSEQ_DIR