| name | plan-first |
|---|---|
| description | Structured planning workflow for any coding task. Use at the start of every new feature, bug fix, refactor, or implementation request. Analyzes the project, asks up to 5 clarifying questions, creates a TODO.md, gets user approval, then executes task by task. Never writes code before a plan is approved. |
| 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"] |
| # 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: |
| # 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 |
| ##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: |