diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -7,31 +7,36 @@ The source code of *cmv* is open source and available via GitHub and Hackage (License GPL-3): -* [![GitHub](https://img.shields.io/github/tag/eggzilla/cmv.svg)](https://github.com/eggzilla/cmv) [![Build Status](https://travis-ci.org/eggzilla/cmv.svg?branch=master)](https://travis-ci.org/eggzilla/cmv) [![Hackage](https://img.shields.io/hackage/v/cmv.svg)](https://hackage.haskell.org/package/cmv) [![Bioconda](https://anaconda.org/bioconda/cmv/badges/version.svg)](https://anaconda.org/bioconda/cmv) +* [![GitHub](https://img.shields.io/github/tag/eggzilla/cmv.svg)](https://github.com/eggzilla/cmv) [![Build Status](https://travis-ci.org/eggzilla/cmv.svg?branch=master)](https://travis-ci.org/eggzilla/cmv) [![Hackage](https://img.shields.io/hackage/v/cmv.svg)](https://hackage.haskell.org/package/cmv) [![Bioconda](https://anaconda.org/bioconda/cmv/badges/version.svg)](https://anaconda.org/bioconda/cmv) [![Docker Repository on Quay](https://quay.io/repository/biocontainers/cmv/status "Docker Repository on Quay")](https://quay.io/repository/repository/biocontainers/cmv) For instruction how to use *cmv* please see the [Help page.](192.52.2.124/cmvs/help) - -### Optional Dependencies: -*cmv* creates output which can be visualised via following optional dependencies. -* [R2R](http://breaker.research.yale.edu/R2R/) -* [forna](http://rna.tbi.univie.ac.at/forna/) ### Installation via bioconda *cmv* can be installed with all dependencies via [conda](https://conda.io/docs/install/quick.html). Once you have conda installed simply type: - conda install -c bioconda cmv=1.0.0 - + conda install -c bioconda -c conda-forge cmv + ### Installation via cabal-install - cmv is implemented in Haskell and can be installed via the Haskell package distribution sytem [cabal](https://www.haskell.org/cabal/). Once you have cabal installed simply type: +cmv is implemented in Haskell and can be installed via the Haskell package distribution sytem [cabal](https://www.haskell.org/cabal/). CMV is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. Additionally to cabal you require [cairo](https://cairographics.org/), [pango](http://www.pango.org/), [happy](https://www.haskell.org/happy/) and [alex](https://www.haskell.org/alex/) which can be installed via the distribution package manager e.g. Ubuntu: + + sudo apt-get install libcairo2 libpango1.0-0 libpangomm-1.4-dev happy alex + +Once you have cabal installed simply type: cabal install cmv +### Optional Dependencies: +*cmv* creates output which can be visualised via following optional dependencies. +* [R2R](http://breaker.research.yale.edu/R2R/) +* [forna](http://rna.tbi.univie.ac.at/forna/) + ### Precompiled Executables -* Linux (ghc-8.0.1) [HMMV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV) -* Linux (ghc-8.0.1) [HMMCV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV) -* Linux (ghc-8.0.1) [CMV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV) -* Linux (ghc-8.0.1) [CMCV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV) +* Linux (ghc-8.0.2) [HMMV 1.0.3 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV) +* Linux (ghc-8.0.2) [HMMCV 1.0.3 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV) +* Linux (ghc-8.0.2) [CMV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV) +* Linux (ghc-8.0.2) [CMCV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV) +* Linux (ghc-8.0.2) [CMCV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCWStoCMCV) diff --git a/changelog b/changelog --- a/changelog +++ b/changelog @@ -1,4 +1,8 @@ -*-change-log-*- +1.0.3 Florian Eggenhofer 12. September 2017 + * Added missing README instructions + * Added link to biocontainer + * Fixed changed dependency in travis file, updated stack file 1.0.2 Florian Eggenhofer 22. June 2017 * Added package meta files for stack and cabal-new 1.0.1 Florian Eggenhofer 16. June 2017 diff --git a/cmv.cabal b/cmv.cabal --- a/cmv.cabal +++ b/cmv.cabal @@ -1,5 +1,5 @@ name: cmv -version: 1.0.2 +version: 1.0.3 synopsis: Detailed visualization of CMs, HMMs and their comparisions description: cmv is a collection of tools for the visualisation of Hidden Markov Models (HMMV) and RNA-family models (CMV). Moreover it can visualise comparisons of these models (HMMCV,CMCV), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure. license: GPL-3 @@ -20,8 +20,8 @@ source-repository this type: git - location: https://github.com/eggzilla/cmv/tree/1.0.2 - tag: 1.0.2 + location: https://github.com/eggzilla/cmv/tree/1.0.3 + tag: 1.0.3 library -- Modules exported by the library. @@ -32,7 +32,7 @@ ghc-options: -Wall -- Other library packages from which modules are imported. - build-depends: base >=4.5 && <5, parsec>=3.1.9, diagrams-lib, BiobaseInfernal, text, vector, ParsecTools, diagrams-cairo, filepath, colour, PrimitiveArray, BiobaseXNA, mtl, directory, either-unwrap, SVGFonts >= 1.6, BioHMM>=1.2.0, StockholmAlignment>=1.1.1, BiobaseTypes,containers + build-depends: base >=4.5 && <5, parsec>=3.1.9, diagrams-lib, BiobaseInfernal, text, vector, ParsecTools, diagrams-cairo, filepath, colour, PrimitiveArray, BiobaseXNA, mtl, directory, either-unwrap, SVGFonts>=1.6.0.2, BioHMM>=1.2.0, StockholmAlignment>=1.1.1, BiobaseTypes,containers,diagrams-core -- Directories containing source files. hs-source-dirs: src @@ -41,31 +41,31 @@ Hs-Source-Dirs: ./src/cmcv/ main-is: CMCVisualisation.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1 + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.4.1.2, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1 executable CMV Hs-Source-Dirs: ./src/cmv/ main-is: CMVisualisation.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1 + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1 executable CMCWStoCMCV Hs-Source-Dirs: ./src/cmcv/ main-is: cmcwsvtocmcv.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath executable CMCtoHMMC Hs-Source-Dirs: ./src/cmcv/ main-is: cmctohmmc.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0 + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0 executable HMMCtoCMC Hs-Source-Dirs: ./src/cmcv/ main-is: hmmctocmc.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0 + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0 executable CMVJson Hs-Source-Dirs: ./src/cmv/ @@ -77,10 +77,10 @@ Hs-Source-Dirs: ./src/hmmcv/ main-is: HMMCVisualisation.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1 + build-depends: base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1 executable HMMV Hs-Source-Dirs: ./src/hmmv/ main-is: HMMVisualisation.hs ghc-options: -Wall - build-depends: base >=4.5, cmdargs, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1 + build-depends: base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1