HPC Software - Text Tools and Software

Flex

Flex is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. The flex program reads user-specified input files, or its standard input if no file names are given, for a description of a scanner to generate. The description is in the form of pairs of regular expressions and C code, called rules. Flex generates a C source file named, "lex.yy.c", which defines the function yylex(). The file "lex.yy.c" can be compiled and linked to produce an executable. When the executable is run, it analyzes its input for occurrences of text matching the regular expressions for each rule. Whenever it finds a match, it executes the corresponding C code. [Flex Website November2014]

Available versions and module name

2.5.39 (flex-2.5.39 or flex)

Default version available

2.5.39

Website

http://flex.sourceforge.net/

If, for whatever reason, you would like to use the older versions of the compilers, or other available software, you can simply "unload" the current module and load the older version. See Software Module Information webpage.

Software list

  • AmpliconNoise
  • ARB
  • BLAST (Legacy BLAST- Not BLAST+)
  • BLAST+
  • Bowtie2
  • CD-HIT
  • cdbtools
  • ChimeraSlayer
  • clearcut
  • Cufflinks
  • Cytoscape
  • FastQC
  • FastTree
  • Fastx-Toolkit
  • Gepard
  • HMMER
  • IGV
  • infernal
  • Kraken
  • metavelvet
  • mothur
  • MUSCLE
  • Ngopt
  • ParsInsert
  • Pear
  • Pplacer
  • QIIME
  • RAxML
  • rRNASelector
  • RSEM
  • RTAX
  • SAM Tools
  • SAMStat
  • SourceTracker
  • TopHat
  • Trimmomatic
  • Trinityrnaseq
  • UCLUST
  • UProC
  • USEARCH
  • Velvet
  • Velvet Optmiser
  • Glasgow Haskell Compiler
  • GNU Bison
  • GNU Compiler
  • GNU Fortran Compiler
  • Go Compiler
  • Intel C and C++ Compiler
  • Intel Fortran Compiler
  • Mono C# Compiler and associated libraries
  • Apache Maven
  • GNU Emacs
  • IntelliJ IDEA
  • RStudio
  • Tex Live
  • Tex Info
  • ANSYS (Fluent and Mechanical)
  • ABAQUS
  • AVL Fire
  • Comsol Multiphysics
  • GDAL
  • GEOS
  • Panoply
  • Circos
  • ImageJ
  • ImageMagick
  • PLPlot
  • Xfig
  • Perl
  • Python (with many Modules Installed)
  • Mathematica
  • Grid Mathematica
  • Matlab
  • Matlab-Simulink
  • Octave
  • OpenBUGS
  • R
  • SPSS (by IBM)
  • Java
  • APSIM
  • Boost C++ Libraries
  • Expat XML Parser
  • FFTW
  • GMP (GNU Multiple Precision Arithmetic Library)
  • GNU Scientific Library (GSL)
  • HDF5
  • HDF-EOS5
  • Intel Math Kernel Libraries (Intel® MKL)
  • libbz2
  • libcurl
  • libjpeg
  • libpng
  • MPI
  • OpenBLAS
  • PCRE (Perl Compatible Regular Expressions)
  • szip
  • tcl
  • tk
  • UDUNITS