From bde64815fb76380144806121c9d4746c34c57f9a Mon Sep 17 00:00:00 2001
From: Brian Yee <bay001@health.ucsd.edu>
Date: Thu, 17 Sep 2026 05:52:21 -0700
Subject: [PATCH] Add rMATS-long v2.1.0 image

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---
 CHANGELOG.md                        |  2 ++
 images/rmats-long/v2.1.0/Dockerfile | 46 +++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100644 images/rmats-long/v2.1.0/Dockerfile

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d1e04d..9d479e5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,5 +13,7 @@
 
 ### Added
 
+- rMATS-long v2.1.0 image (`images/rmats-long/v2.1.0/Dockerfile`), built from
+  the upstream release tag with Miniforge; publishes `ghcr.io/yeolab/rmats-long:v2.1.0`.
 - GitHub Actions publishing of changed Dockerfiles to GitHub Container Registry
   (GHCR), including source, SBOM, and provenance metadata.
diff --git a/images/rmats-long/v2.1.0/Dockerfile b/images/rmats-long/v2.1.0/Dockerfile
new file mode 100644
index 0000000..1fffe32
--- /dev/null
+++ b/images/rmats-long/v2.1.0/Dockerfile
@@ -0,0 +1,46 @@
+################## BASE IMAGE ######################
+
+FROM debian:trixie
+
+################## METADATA ######################
+
+LABEL base_image="debian:trixie"
+LABEL version="1"
+LABEL software="rmats-long"
+LABEL software.version="v2.1.0"
+LABEL about.summary="Differential isoform and alternative splicing module analysis for long-read RNA-seq"
+LABEL about.url="https://github.com/Xinglab/rMATS-long"
+LABEL about.license="MIT"
+LABEL about.license_file="https://github.com/Xinglab/rMATS-long/blob/main/LICENSE"
+LABEL about.tags="Genomics,Transcriptomics,Long-read"
+
+ARG RMATS_LONG_VERSION=v2.1.0
+
+# Mirrors the upstream Dockerfile (github.com/Xinglab/rMATS-long), but pins the
+# release tag and uses Miniforge (conda-forge only) so no channel ToS prompt is needed.
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       ca-certificates \
+       curl \
+       git \
+       procps \
+    && rm -rf /var/lib/apt/lists/* \
+    && mkdir /conda \
+    && cd /conda \
+    && curl -L 'https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh' -o miniforge.sh \
+    && bash miniforge.sh -b -p /conda/install \
+    && rm miniforge.sh \
+    && /conda/install/bin/conda init \
+    && git clone --depth 1 --branch "${RMATS_LONG_VERSION}" 'https://github.com/Xinglab/rMATS-long.git' /rMATS-long \
+    && cd /rMATS-long \
+    && ./install \
+    && /conda/install/bin/conda clean -afy
+
+ENV PATH=/rMATS-long/conda_env/bin:${PATH}
+
+# Set defaults for running the image.
+# The ENTRYPOINT and CMD are empty to be compatible with
+# CWL and WDL implementations that cannot override those values
+WORKDIR /rMATS-long
+ENTRYPOINT []
+CMD []