From 15b6c8abc15261d3e133e65cb8321c9face71bd6 Mon Sep 17 00:00:00 2001
From: Shixiang Wang <wangshx@shanghaitech.edu.cn>
Date: Tue, 23 Jan 2024 15:11:26 +0800
Subject: [PATCH] update desc & readme

---
 DESCRIPTION | 5 +++--
 Dockerfile  | 2 +-
 README.md   | 8 ++++++++
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1757e8c..4f1b6d4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,8 @@ Description: Provides data processing pipeline feeding paired bam files
     and XGBOOST model for predicting tumor circular amplicons (also known
     as ecDNA) in gene level.
 License: Non-Commercial Academic License + file LICENSE
-URL: https://github.com/ShixiangWang/gcap, https://shixiangwang.github.io/gcap/
+URL: https://github.com/ShixiangWang/gcap,
+    https://shixiangwang.github.io/gcap/
 BugReports: https://github.com/ShixiangWang/gcap/issues
 Depends: 
     ASCAT (>= 3.0.0),
@@ -44,9 +45,9 @@ LinkingTo:
     Rcpp
 Remotes: 
     bitbucket::sequenzatools/sequenza,
+    github::ShixiangWang/ascat/ASCAT@v3-for-gcap-v1,
     github::ShixiangWang/copynumber,
     github::ShixiangWang/facets,
-    github::ShixiangWang/ascat/ASCAT@v3-for-gcap-v1,
     github::ShixiangWang/IDConverter
 biocViews:
 Config/testthat/edition: 3
diff --git a/Dockerfile b/Dockerfile
index 900e088..5970295 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -18,7 +18,7 @@ RUN apt update && apt install -y build-essential zip cmake libcairo2-dev &&\
 # Install GCAP & deploy it
 # XGBOOST should be <1.6
 # The default path for conda in the container is /opt/conda
-RUN mamba install -y -c conda-forge -c bioconda r-base=4.2 python=3.8 r-remotes r-biocmanager r-tidyverse r-sigminer sequenza-utils samtools tabix  &&\
+RUN mamba install -y -c conda-forge -c bioconda r-base=4.3 python=3.10 r-remotes r-biocmanager r-tidyverse r-sigminer sequenza-utils samtools tabix  &&\
     mamba clean -yaf &&\
     R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/xgboost/xgboost_1.5.2.1.tar.gz", repos = NULL)' &&\
     R -e 'BiocManager::install("jokergoo/GetoptLong", update = FALSE, force = TRUE)' &&\
diff --git a/README.md b/README.md
index d9c4b61..645e9c7 100644
--- a/README.md
+++ b/README.md
@@ -207,6 +207,14 @@ functions as they are not exported from **gcap**.
 > gcap:::cat_log_file()
 ```
 
+## Docker image
+
+A docker image is available in [ghcr](https://github.com/ShixiangWang/gcap/pkgs/container/gcap) along with its corresponding [Dockerfile](https://github.com/ShixiangWang/gcap/blob/master/Dockerfile). This image comes pre-installed with all the necessary software. However, users are responsible for mapping the required reference files and input data files on their own. The Dockerfile can be customized according to the user's specific requirements, as permitted by the license we provide.
+
+```sh
+docker pull ghcr.io/shixiangwang/gcap:latest
+```
+
 ## Related tools
 
 - [gcaputils](https://github.com/ShixiangWang/gcaputils): **gcap** utils for downstream analysis and visualization.