update desc & readme

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

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)' &&\

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.