harish0201

FROM rhub/r-minimal
RUN installr -d -a "curl-dev gfortran libjpeg-turbo-dev libpng-dev libpng libjpeg-turbo" ggplot2 cowplot clusterProfiler org.Hs.eg.db org.Mm.eg.db org.Cf.eg.db org.Sc.sgd.db
&& apk del --no-cache
WORKDIR /data
RUN mkdir -p /data/in /data/out
COPY ClusterProfiler_Enrichment.R /data/
ENV PATH=$PATH:/data/:/usr/bin:/bin
ENTRYPOINT [ "Rscript", "/data/ClusterProfiler_Enrichment.R"]

harish0201

# The build-stage image:
FROM continuumio/miniconda3 AS build

# Install the package as normal:
COPY environment.yml ClusterProfiler_Enrichment.R /
RUN conda install -y -c conda-forge mamba && mamba env create -f environment.yml

# Install conda-pack
# Use conda-pack to create a standalone enviornment
# in /venv:

harish0201

# see below for UPDATES that include more shorter ways of conversions

# How to convert GTF format into BED12 format (Human-hg19)?
# How to convert GTF or BED format into BIGBED format?
# Why BIGBED (If GTF or BED file is very large to upload in UCSC, you can use trackHubs. However trackHubs do not accept either of the formats. Therefore you would need bigBed format)

# First, download UCSC scripts
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed

harish0201

##Assumes that Anaconda/Miniconda etc are installed: 
#Credit to Donovan Parks at STAMP Google Group

#1. Deactivate all the environments loaded
conda deactivate

#2. Create a new environment for stamp:
conda create -y -n stamp-test python=2.7

#3. Install all the dependencies: