diff --git a/misc/Dockerfile b/misc/Dockerfile new file mode 100644 index 0000000..b2f11a1 --- /dev/null +++ b/misc/Dockerfile @@ -0,0 +1,44 @@ +FROM ubuntu:22.04 + +MAINTAINER Jeltje van Baren, jeltje.van.baren@gmail.com + +# deal with tzdata timezone question +# see https://dev.to/setevoy/docker-configure-tzdata-and-timezone-during-build-20bk +ENV TZ=America/Los_Angeles +RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone + +#Install Essentials +RUN apt-get update && apt-get install -y \ + wget \ + build-essential \ + cmake \ + git \ + pkg-config \ + libcurl4-openssl-dev \ + libssl-dev \ + libxml2-dev \ + samtools \ + bedtools \ + minimap2 \ + r-base \ + salmon \ + python3 \ + python3-pip + +RUN pip install flair-brookslab==1.6.3 \ + rpy2 \ + pandas \ + matplotlib \ + seaborn + +RUN R -e 'update.packages(ask=FALSE)' +RUN R -e 'install.packages(c("devtools", "BiocManager", "ggplot2", "qqman", "lazyeval"))' +RUN R -e 'requireNamespace("BiocManager"); BiocManager::install(c("DRIMSeq", "stageR", "DESeq2", "apeglm"))' + +RUN mkdir /data +WORKDIR /data + +# And clean up +RUN apt-get clean && rm -rf /var/lib/apt/lists/* + + diff --git a/setup.cfg b/setup.cfg index 4ca9e4d..8a3cf2e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = flair-brookslab -version = 1.6.2 +version = 1.6.3 author = Jeltje van Baren author_email = jeltje.van.baren@gmail.com description = flair diff --git a/src/flair/flair.py b/src/flair/flair.py index e3b451d..a0f9e52 100755 --- a/src/flair/flair.py +++ b/src/flair/flair.py @@ -1182,7 +1182,7 @@ def main(): sys.exit(1) if mode == '--version': - sys.stderr.write('FLAIR v1.6.2\n') + sys.stderr.write('FLAIR v1.6.3\n') if __name__ == "__main__":