remove salmon and add STAR

Author: jen-reeve

docker/Dockerfile

@@ -133,21 +133,12 @@ RUN apt-get update && apt-get install -y cmake && \
     apt-get clean && rm -rf /var/lib/apt/lists/* && \
     bamtools --version
 
-# Install salmon
-RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz && \
-    tar -xzf salmon-1.10.0_linux_x86_64.tar.gz  && \
-    cp -r salmon-latest_linux_x86_64/bin/* /usr/local/bin/ && \
-    cp -r salmon-latest_linux_x86_64/lib/* /usr/local/lib/ && \
-    rm -rf salmon-1.10.1* && \
-    salmon --version
-
-
-# # Install STAR with required dependencies
-# RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11b.zip && \
-#     unzip STAR_2.7.11b.zip && \
-#     cp STAR_2.7.11b/Linux_x86_64/STAR* /usr/local/bin/ && \
-#     rm -rf STAR_2.7.11b* && \
-#     STAR --version
+# Install STAR with required dependencies
+RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11b.zip && \
+    unzip STAR_2.7.11b.zip && \
+    cp STAR_2.7.11b/Linux_x86_64/STAR* /usr/local/bin/ && \
+    rm -rf STAR_2.7.11b* && \
+    STAR --version
 
 # install R packages
 RUN Rscript -e 'install.packages("BiocManager", repos = "https://cloud.r-project.org")' \