cmv 1.0.5 → 1.0.6
raw patch · 4 files changed
+15/−8 lines, 4 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- README.md +7/−1
- changelog +2/−0
- cmv.cabal +4/−4
- src/hmmcv/HMMCVisualisation.hs +2/−3
README.md view
@@ -10,7 +10,13 @@ * [](https://github.com/eggzilla/cmv) [](https://travis-ci.org/eggzilla/cmv) [](https://hackage.haskell.org/package/cmv) [](https://anaconda.org/bioconda/cmv) [](https://quay.io/repository/repository/biocontainers/cmv) For instruction how to use *cmv* please see the [Help page.](192.52.2.124/cmvs/help)- ++### Usage via biocontainer (docker)++*cmv* can be retrieved and used as docker container with all dependencies via [docker](https://docs.docker.com/engine/installation/). Once you have docker installed simply type:++ docker run -i -t quay.io/biocontainers/cmv:1.0.5--0 /bin/bash+ ### 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:
changelog view
@@ -1,4 +1,6 @@ -*-change-log-*-+1.0.6 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 26. September 2017+ * Fixed a missing output bug in HMMCV 1.0.5 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 18. September 2017 * Changed used stack lts due to problems with build tool dependencies 1.0.4 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 14. September 2017
cmv.cabal view
@@ -1,12 +1,12 @@ name: cmv-version: 1.0.5+version: 1.0.6 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 license-file: LICENSE author: Florian Eggenhofer maintainer: egg@informatik.uni-freiburg.de-Tested-With: GHC == 7.10.3, GHC == 8.0.2, GHC == 8.2.1 +Tested-With: GHC == 8.0.2, GHC == 8.2.1 category: Bioinformatics build-type: Simple cabal-version: >=1.8@@ -20,8 +20,8 @@ source-repository this type: git- location: https://github.com/eggzilla/cmv/tree/1.0.5- tag: 1.0.5+ location: https://github.com/eggzilla/cmv/tree/1.0.6+ tag: 1.0.6 library -- Modules exported by the library.
src/hmmcv/HMMCVisualisation.hs view
@@ -54,7 +54,7 @@ outputFormat = "pdf" &= name "f" &= help "Output image format: pdf, svg, png, ps (Default: pdf)", outputDirectoryPath = "" &= name "p" &= help "Output directory path (Default: none)", modelNameToggle = False &= name "b" &= help "Write all comma separted model names to modelNames file (Default: False)"- } &= summary ("HMMCV " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2016" &= verbosity+ } &= summary ("HMMCV " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2017" &= verbosity main :: IO () main = do@@ -63,7 +63,7 @@ modelFileExists <- doesFileExist modelsFile hmmCFileExists <- doesFileExist hmmCompareResultFile alnFileExists <- doesFileExist alignmentFile- if modelFileExists && hmmCFileExists && alnFileExists+ if modelFileExists && hmmCFileExists then do inputModels <- HM.readHMMER3 modelsFile if isRight inputModels@@ -80,7 +80,6 @@ if and $ map isRight hmmCResultParsed then do let rightHMMCResultsParsed = rights hmmCResultParsed- --let outputName = diagramName "hmmcv" outputFormat setCurrentDirectory dirPath let modelFileNames = map (\m -> m ++ "." ++ outputFormat) currentModelNames let alignmentFileNames = map (\m -> m ++ ".aln" ++ "." ++ outputFormat) currentModelNames