biohazard-0.6.6: biohazard.cabal
Name: biohazard
Version: 0.6.6
Synopsis: bioinformatics support library
Description: This is a collection of modules I separated from
various bioinformatics tools. The hope is to make
them reusable and easier to maintain. Also includes
some of these tools and a bunch that work on mitochondrial
sequences.
Category: Bioinformatics
Homepage: http://github.com/udo-stenzel/biohazard
License: BSD3
License-File: LICENSE
Author: Udo Stenzel
Maintainer: udo.stenzel@eva.mpg.de
Copyright: (C) 2010-2016 Udo Stenzel
Extra-Source-Files: man/man7/biohazard.7
man/man1/bam-meld.1
man/man1/bam-rewrap.1
man/man1/bam-rmdup.1
man/man1/jivebunny.1
man/man1/mt-anno.1
doc/genotyping.tex
Data-Files: index_db.json
Data-Dir: data
Cabal-version: >=1.9.2
Build-type: Custom
-- Tested-With: GHC == 7.4.2, GHC == 7.6.3, GHC == 7.8.4, GHC == 7.10.3
source-repository head
type: git
location: https://bitbucket.org/ustenzel/biohazard.git
source-repository this
type: git
location: https://bitbucket.org/ustenzel/biohazard.git
tag: 0.6.6
Library
Exposed-modules: Bio.Base,
Bio.Adna,
Bio.Align,
Bio.Bam,
Bio.Bam.Evan,
Bio.Bam.Fastq,
Bio.Bam.Filter,
Bio.Bam.Header,
Bio.Bam.Index,
Bio.Bam.Pileup,
Bio.Bam.Regions,
Bio.Bam.Reader
Bio.Bam.Rec,
Bio.Bam.Rmdup,
Bio.Bam.Trim,
Bio.Bam.Writer,
Bio.Genocall,
Bio.Genocall.AvroFile,
Bio.Genocall.Metadata,
Bio.Iteratee,
Bio.Iteratee.Bgzf,
Bio.Iteratee.Builder,
Bio.Iteratee.ZLib,
Bio.PriorityQueue,
Bio.TwoBit,
Bio.Util.AD,
Bio.Util.AD2,
Bio.Util.Numeric,
Bio.Util.Regex,
Data.MiniFloat,
Data.Avro
Other-modules: Paths_biohazard
Build-depends: aeson >= 0.7 && < 0.9,
async == 2.0.*,
attoparsec >= 0.10 && < 0.13,
base >= 4.5 && < 4.10,
binary >= 0.7 && < 0.9,
bytestring >= 0.10.2 && < 0.11,
bytestring-mmap >= 0.2 && < 1.0,
containers >= 0.4.1 && < 0.6,
deepseq >= 1.3 && < 1.5,
directory >= 1.2 && < 2.0,
exceptions >= 0.6 && < 0.9,
filepath >= 1.3 && < 2.0,
iteratee >= 0.8.9.6 && < 0.8.10,
ListLike >= 3.0 && < 5.0,
nonlinear-optimization == 0.3.*,
primitive >= 0.5 && < 0.7,
random >= 1.0 && < 1.2,
scientific == 0.3.*,
stm == 2.4.*,
template-haskell == 2.*,
text >= 1.0 && < 2.0,
transformers >= 0.3 && < 0.6,
unix >= 2.5 && < 2.8,
unordered-containers >= 0.2.3 && < 0.3,
Vec == 1.*,
vector >= 0.9 && < 0.11,
vector-algorithms >= 0.3 && < 1.0,
vector-th-unbox == 0.2.*,
zlib >= 0.5 && < 0.7
Ghc-options: -Wall
Hs-source-dirs: src
Install-Includes: src/cbits/myers_align.h
C-sources: src/cbits/myers_align.c
CC-options: -fPIC
-- Modules not exported by this package.
-- Other-modules:
-- Extra tools (e.g. alex, hsc2hs, ...) needed to build the source.
-- Build-tools:
-- Test-Suite test-biohazard
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
-- Type: exitcode-stdio-1.0
-- Main-is: test-biohazard.hs
Executable redeye-dar
Main-is: redeye-dar.hs
Hs-Source-Dirs: tools
Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Build-depends: async,
base,
biohazard,
filepath,
unordered-containers,
text,
vector
Executable redeye-div
Main-is: redeye-div.hs
Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Hs-Source-Dirs: tools
Build-depends: async,
base,
biohazard,
filepath,
hmatrix == 0.16.*,
unordered-containers,
text,
vector
Executable redeye-pileup
Main-is: redeye-pileup.hs
Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Hs-Source-Dirs: tools
Build-depends: aeson,
base,
biohazard,
bytestring,
containers,
directory,
filepath,
iteratee,
text,
unordered-containers,
Vec,
vector
Executable redeye-single
Main-is: redeye-single.hs
Ghc-options: -Wall -rtsopts
Hs-Source-Dirs: tools
Build-depends: aeson,
base,
biohazard,
bytestring,
containers,
directory,
iteratee,
filepath,
text,
unix,
unordered-containers,
vector
Executable gt-scan
Main-is: gt-scan.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
Build-depends: aeson,
base,
biohazard,
bytestring,
containers,
iteratee,
nonlinear-optimization,
primitive,
strict == 0.3.*,
unordered-containers,
text,
vector
-- ------
Executable afroengineer
Main-is: afroengineer.hs
Ghc-options: -Wall
Hs-source-dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Other-Modules: Align, SimpleSeed
Build-Depends: base,
biohazard,
bytestring,
containers,
directory,
iteratee,
unordered-containers,
vector
Executable bam-fixpair
Main-is: bam-fixpair.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
binary,
biohazard,
bytestring,
hashable >= 1.0 && < 1.3,
transformers,
vector
Executable bam-meld
Main-is: bam-meld.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
biohazard,
bytestring,
containers
Executable bam-resample
Main-is: bam-resample.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
biohazard,
bytestring,
random
Executable bam-rewrap
Main-is: bam-rewrap.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
biohazard,
bytestring,
containers
Executable bam-rmdup
Main-is: bam-rmdup.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
biohazard,
bytestring,
containers,
iteratee,
unordered-containers,
vector,
vector-algorithms
Executable bam-trim
Main-is: bam-trim.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
biohazard,
bytestring
Executable fastq2bam
Main-is: fastq2bam.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-depends: base,
biohazard,
bytestring,
containers,
iteratee,
vector
Executable jivebunny
Main-is: jivebunny.hs
Hs-Source-Dirs: tools
C-sources: src/cbits/jive.c
CC-options: -std=c99 -ffast-math
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Other-modules: Index
Build-depends: aeson,
base,
biohazard,
bytestring,
containers,
directory,
hashable >= 1.0 && < 1.3,
random,
text,
transformers,
unordered-containers,
vector,
vector-algorithms,
vector-th-unbox
Executable mt-anno
Main-is: mt-anno.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Other-Modules: Anno, Seqs, Xlate
Build-Depends: base,
bytestring,
biohazard,
containers
Executable mt-ccheck
Main-is: mt-ccheck.hs
Ghc-options: -Wall
Hs-Source-Dirs: tools
-- Ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
Ghc-options: -Wall -rtsopts
Build-Depends: base,
bytestring,
biohazard,
containers,
unordered-containers
-- :vim:tw=132: