clustertools-0.1.1: clustertools.cabal

Name:                clustertools
Version:             0.1.1
License:             GPL
License-file:        LICENSE
Author:              Ketil Malde
Maintainer:          Ketil Malde <ketil@malde.org>

Category:            Bioinformatics
Synopsis:            Tools for manipulating sequence clusters
Description:         This is a bunch of stuff I needed at some for manipulating sequence
                     clusters. See the README for details. The tools included are:
                     .
                     * filter - remove unwanted sequences from a clustering
                     .
                     * hist   - produce a histogram of cluster sizes from a "label"-formatted clustering.
                     .
                     * clusc  - compare clusterings, calculating numerous pair-based and entropy based indices.
                     .
                     * add_single - add singletons to a clustering.
                     .
                     * ace2contigs - parse an ACE assembly file, and output the contigs in a FASTA file.
                     .
                     * ace2fasta - parse an ACE assembly, and output each assembly in a separate FASTA file
                     .
		     * ace2clusters - parse an ACE assembly, and output clusters in TGICL format
		     .
                     * clusterlibs - given a table of regular expressions and library names, along with a
                     clustering (TGICL-format), output a table of clusters with the library name
                     prepended to the sequences.
                     .
		     * xcerpt - extract sequences from a list of sequence labels.
		     .
                     The Darcs repository is at: <http://malde.org/~ketil/biohaskell/cluster_tools>.
Homepage:            http://malde.org/~ketil/

Tested-With:         GHC==6.8.2
Build-Type:          Simple
Cabal-Version:       >= 1.2

Data-Files:          README

Executable filter
           Hs-source-dirs: src
           Main-Is:     Filter.hs
           Build-Depends:       base>3, containers, simpleargs>=0.1
           ghc-options:         -Wall -O2 -funbox-strict-fields

Executable clusc
           Hs-source-dirs: src
           Main-Is:     Cluscomp.lhs
           Build-Depends: bytestring

Executable add_single
           Hs-source-dirs: src
           Main-Is:     AddSingletons.hs

Executable ace2contigs
           Hs-source-dirs: src
           Main-Is:     Ace2Contigs.hs
           Build-depends: bio>=0.3.3.4

Executable ace2fasta
           Hs-source-dirs: src
           Main-Is:     Ace2Fasta.hs
           Build-depends: bio>=0.3.3.4

Executable ace2clusters
           Hs-source-dirs: src
           Main-Is:     Ace2Clusters.hs
           Build-depends: bio>=0.3.3.4

Executable clusterlibs
           Hs-source-dirs: src
           Main-Is:     ClusterLibs.hs
           Build-depends: regex-compat

Executable xcerpt
           Hs-source-dirs: src
           Main-Is:     Xcerpt.lhs
           Build-depends: haskell98