From 67f1d47b3e5e1d29c103b02a8f6b489e1af95fcb Mon Sep 17 00:00:00 2001
From: Yiming Yang <yang.yihming@gmail.com>
Date: Mon, 17 Apr 2023 23:06:50 -0700
Subject: [PATCH] upgrade star version to 2.7.10b

---
 docker/starsolo/2.7.10a/Dockerfile       |  8 ++--
 docker/starsolo/2.7.10b/Dockerfile       | 50 ++++++++++++++++++++++++
 workflows/starsolo/starsolo_workflow.wdl |  4 +-
 3 files changed, 56 insertions(+), 6 deletions(-)
 create mode 100644 docker/starsolo/2.7.10b/Dockerfile

diff --git a/docker/starsolo/2.7.10a/Dockerfile b/docker/starsolo/2.7.10a/Dockerfile
index 2d01ee04..a5889fff 100644
--- a/docker/starsolo/2.7.10a/Dockerfile
+++ b/docker/starsolo/2.7.10a/Dockerfile
@@ -28,11 +28,11 @@ RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.6.4.zip" -o "aw
     ./aws/install && \
     rm awscliv2.zip
 
-RUN wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.10a_alpha_220601.tar.gz && \
-    tar -xzvf 2.7.10a_alpha_220601.tar.gz && \
-    rm 2.7.10a_alpha_220601.tar.gz && \
+RUN wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.10a_alpha_220818.tar.gz && \
+    tar -xzvf 2.7.10a_alpha_220818.tar.gz && \
+    rm 2.7.10a_alpha_220818.tar.gz && \
     mkdir /software && \
-    mv STAR-2.7.10a_alpha_220601 /software/STAR && \
+    mv STAR-2.7.10a_alpha_220818 /software/STAR && \
     cd /software/STAR/source && \
     make STAR && \
     mkdir -p /software/STAR/bin && \
diff --git a/docker/starsolo/2.7.10b/Dockerfile b/docker/starsolo/2.7.10b/Dockerfile
new file mode 100644
index 00000000..99a70207
--- /dev/null
+++ b/docker/starsolo/2.7.10b/Dockerfile
@@ -0,0 +1,50 @@
+FROM debian:bullseye-slim
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get -qq update && \
+    apt-get -qq -y install --no-install-recommends \
+        wget \
+        build-essential \
+        curl \
+        zlib1g-dev \
+        unzip \
+        gnupg \
+        python3 \
+        python3-pip
+
+RUN pip3 install --upgrade pip --no-cache-dir && \
+    pip3 install numpy==1.24.2 --no-cache-dir && \
+    pip3 install pandas==2.0.0 --no-cache-dir && \
+    pip3 install h5py==3.8.0 --no-cache-dir && \
+    pip3 install pegasusio==0.8.0 --no-cache-dir && \
+    pip3 install stratocumulus==0.1.7 --no-cache-dir
+
+RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
+    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \
+    apt-get update -y && apt-get install -y google-cloud-cli=426.0.0-0
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.11.13.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && \
+    ./aws/install && \
+    rm awscliv2.zip
+
+RUN wget https://github.com/alexdobin/STAR/archive/refs/tags/STAR_2.7.10b_alpha_230301.tar.gz && \
+    tar -xzvf STAR_2.7.10b_alpha_230301.tar.gz && \
+    rm STAR_2.7.10b_alpha_230301.tar.gz && \
+    mkdir /software && \
+    mv STAR-STAR_2.7.10b_alpha_230301 /software/STAR && \
+    cd /software/STAR/source && \
+    make STAR && \
+    mkdir -p /software/STAR/bin && \
+    ln -s /software/STAR/source/STAR /software/STAR/bin/STAR
+
+RUN apt-get -qq -y remove curl gnupg wget curl && \
+    apt-get -qq -y autoremove && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /var/log/dpkg.log && \
+    ln -s /usr/bin/python3 /usr/bin/python
+
+ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software
+RUN chmod a+rx /software/monitor_script.sh
+
+ENV PATH=/software:/software/STAR/bin:$PATH
diff --git a/workflows/starsolo/starsolo_workflow.wdl b/workflows/starsolo/starsolo_workflow.wdl
index b9f6c200..57ef214c 100644
--- a/workflows/starsolo/starsolo_workflow.wdl
+++ b/workflows/starsolo/starsolo_workflow.wdl
@@ -64,8 +64,8 @@ workflow starsolo_workflow {
         String? soloOutFormatFeaturesGeneField3
         # Number of CPUs to request per sample
         Int num_cpu = 32
-        # STAR version to use. Currently support: 2.7.10a
-        String star_version = "2.7.10a"
+        # STAR version to use. Currently support: 2.7.10b
+        String star_version = "2.7.10b"
         # Docker registry, default to quay.io/cumulus
         String docker_registry = "quay.io/cumulus"
         # Reference Index TSV