From 7c4333db00d80df09b8f2cc157e10e2cd3cee33a Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 19 Nov 2024 11:58:16 -0500
Subject: [PATCH] ci: use older miniforge release

---
 Dockerfile | 35 +++++++++++++++++++++++++++++++----
 1 file changed, 31 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 2ee745b..46ab6de 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM python:3.7.17-bookworm
 
 RUN mkdir -p /opt2 && mkdir -p /data2
 ENV TZ=America/New_York
@@ -22,15 +22,43 @@ RUN apt-get update && apt-get install -y \
   wget
 
 # Install conda and give write permissions to conda folder
+ENV miniforge_version="23.3.1-1" 
 RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
-    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/${miniforge_version}/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
     /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
     rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
 ENV PATH=$PATH:/opt2/conda/bin
 # install most mimseq deps from conda
 RUN mamba install -c bioconda -c conda-forge \
     python=3.7 \
-    mimseq
+    'r-base>=4.1' \
+    'biopython>=1.79' \
+    'matplotlib-base>=3.4.2' \
+    'numpy>=1.21.1' \
+    'pandas>=1.3.1' \
+    'requests>=2.26.0' \
+    'pybedtools>=0.8.2' \
+    'pyfiglet>=0.8.post1' \
+    'pysam>=0.16.0.1' \
+    'seaborn-base>=0.11.1' \
+    'statsmodels>=0.13.1' \
+    'infernal>=1.1.4' \
+    'blast>=2.10.1' \
+    'gmap>=2018.03.20,<=2019.02.26' \
+    'samtools>=1.11' \
+    'bedtools>=2.30.0' \
+    'r-ggplot2>=3.3.5' \
+    'r-ggpol>=0.0.7' \
+    'bioconductor-complexheatmap>=2.2.0' \
+    'bioconductor-deseq2>=1.26.0' \
+    'r-pheatmap>=1.0.12' \
+    'r-calibrate>=1.7.7' \
+    'r-gridextra>=2.3' \
+    'r-plyr>=1.8.6' \
+    'r-dplyr>=1.0.6' \
+    'r-tidyverse>=1.3.0' \
+    'r-devtools>=2.4.1' \
+    'r-reshape2>=1.4.4'
 
 # install usearch
 RUN wget https://drive5.com/downloads/usearch10.0.240_i86linux32.gz && \
@@ -47,7 +75,6 @@ WORKDIR /opt2/mim-tRNAseq
 RUN pip install --upgrade pip && \
   pip install . && \
   mimseq --version
-  ENV PATH=/opt2/mim-tRNAseq:$PATH
 
 # check mimseq installation
 WORKDIR /opt2