diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..de149a88d5f53c9f2b96b81d84d60b035cea8e59 --- /dev/null +++ b/.gitignore @@ -0,0 +1,61 @@ +# Created by https://www.toptal.com/developers/gitignore/api/r +# Edit at https://www.toptal.com/developers/gitignore?templates=r + +### R ### +# History files +.Rhistory +.Rapp.history + +# Session Data files +.RData +.RDataTmp + +# User-specific files +.Ruserdata + +# Example code in package build process +*-Ex.R + +# Output files from R CMD build +/*.tar.gz + +# Output files from R CMD check +/*.Rcheck/ + +# RStudio files +.Rproj.user/ + +# produced vignettes +vignettes/*.html +vignettes/*.pdf + +# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 +.httr-oauth + +# knitr and R markdown default cache directories +*_cache/ +/cache/ + +# Temporary files created by R markdown +*.utf8.md +*.knit.md + +# R Environment Variables +.Renviron + +# pkgdown site +docs/ + +# translation temp files +po/*~ + +# RStudio Connect folder +rsconnect/ + +### R.Bookdown Stack ### +# R package: bookdown caching files +/*_files/ + +# End of https://www.toptal.com/developers/gitignore/api/r +tests/test_files/test.fa.gz.fai +tests/test_files/test.fa.gz.gzi diff --git a/README.md b/README.md index a0fd5bc9cce27f0be25794881b089843defbf021..7c75a71a58aa6bfe831513e2d1f37f57ded5959a 100644 --- a/README.md +++ b/README.md @@ -13,16 +13,26 @@ ascii_alignment_pileup.R [-hv] [OPTIONS] bed bam [bam2 ...] ## Requirements -* `R` 3.6.0 / 4.2.1 +* `R` 3.6.0 / 4.1.3 / 4.2.1 * `optparse` 1.6.2 / 1.7.1 -* `rtracklayer` 1.44.0 / 1.56.1 +* `rtracklayer` 1.44.0 / 1.54.0 / 1.56.1 The script was successfully tested with the indicated versions. Other versions may work as well, but have not been tested. -For convenience, you can build a container with all required software from the -provided `Dockerfile` with `docker build .`. Alternatively, you can also pull a -prebuilt Docker image from +## Installation + +The easiest way to install the script is via [Conda][conda]. If you have Conda +installed, all you need to do is: + +``` +conda env create -f environment.yml +conda activate ascii-alignment-pileup +``` + +Alternatively, you can build a container with all required software from the +provided `Dockerfile` with `docker build .`. You can also pull a prebuilt +Docker image from <https://hub.docker.com/repository/docker/zavolab/ascii-alignment-pileup>. ## Input files @@ -204,6 +214,7 @@ Email: <zavolab-biozentrum@unibas.ch> [bed]: <https://www.ensembl.org/info/website/upload/bed.html> [bgzip]: <http://www.htslib.org/doc/bgzip.html> [biocontainers]: <https://biocontainers.pro/> +[conda]: <https://docs.conda.io/en/latest/> [fasta]: <https://en.wikipedia.org/wiki/FASTA_format> [gff]: <https://en.wikipedia.org/wiki/General_feature_format> -[htslib]: <https://github.com/samtools/htslib> \ No newline at end of file +[htslib]: <https://github.com/samtools/htslib> diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000000000000000000000000000000000000..3452990d3e3ae7a475f63debd191e66c83a857ed --- /dev/null +++ b/environment.yml @@ -0,0 +1,6 @@ +name: ascii-alignment-pileup +channels: + - bioconda +dependencies: + - r-optparse=1.7.1 + - bioconductor-rtracklayer=1.54.0 diff --git a/tests/test.sh b/tests/test.sh index 0ccc00933907d5ad514d3fe3f3ac757848b3b475..76a5864bc7d69c6bf96462f374ff0d5d0fc87936 100755 --- a/tests/test.sh +++ b/tests/test.sh @@ -17,7 +17,7 @@ user_dir=$PWD script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)" cd $script_dir -ascii_alignment_pileup.R \ +../ascii_alignment_pileup.R \ --verbose \ --reference="test_files/test.fa.gz" \ --annotations="test_files/test.gff" \