Added samtools and Google Cloud SDK

Dockerfile

@@ -19,8 +19,11 @@ RUN apt-get update -yq \
     tabix \
     unzip \
     python3 \
-    python3-pip
-
+    python3-pip \
+    libncurses5-dev 
+
+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 google-cloud-sdk -y      
+
 RUN python3 -m pip install -U matplotlib==3.2.2
 
 RUN wget -q https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2 \
@@ -57,6 +60,17 @@ RUN wget -q https://github.com/samtools/bcftools/releases/download/1.9/bcftools-
 
 ENV PATH="$PATH:/bcftools"
 
+RUN wget -q https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2 \
+ && tar xvjf samtools-1.14.tar.bz2 \
+ && cd samtools-1.14 \
+ && ./configure --prefix=/samtools \
+ && make \
+ && make install \
+ && cd / \
+ && rm -rf samtools-1.14*
+
+ENV PATH="$PATH:/samtools/bin"
+
 RUN wget -q https://github.com/odelaneau/GLIMPSE/archive/refs/tags/v1.1.1.zip \
  && unzip v1.1.1.zip \
  && mv GLIMPSE-1.1.1 GLIMPSE \
@@ -67,17 +81,19 @@ RUN wget -q https://github.com/odelaneau/GLIMPSE/archive/refs/tags/v1.1.1.zip \
  && sed -i "s/system: DYN_LIBS=.*/system: DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lssl -lcrypto/g" /GLIMPSE/sample/makefile \
  && sed -i "s/system: DYN_LIBS=.*/system: DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lssl -lcrypto/g" /GLIMPSE/concordance/makefile
 
+ENV PATH="$PATH:/GLIMPSE/chunk/bin:/GLIMPSE/concordance/bin:/GLIMPSE/ligate/bin:/GLIMPSE/phase/bin:/GLIMPSE/sample/bin"
+
 WORKDIR /GLIMPSE/tutorial
 
-RUN ./step1_script_setup.sh
-RUN ./step2_script_reference_panel.sh  
-RUN ./step3_script_GL.sh  
-RUN ./step4_script_chunk.sh  
-RUN ./step5_script_impute.sh  
-RUN ./step6_script_ligate.sh  
-RUN ./step7_script_sample.sh  
-RUN ./step8_script_concordance.sh 
-RUN ./step9_script_cleanup.sh
+RUN /GLIMPSE/tutorial/step1_script_setup.sh
+# RUN ./step2_script_reference_panel.sh  
+# RUN ./step3_script_GL.sh  
+# RUN ./step4_script_chunk.sh  
+# RUN ./step5_script_impute.sh  
+# RUN ./step6_script_ligate.sh  
+# RUN ./step7_script_sample.sh  
+# RUN ./step8_script_concordance.sh 
+# RUN ./step9_script_cleanup.sh
 
 WORKDIR /
 

README.md

@@ -5,15 +5,17 @@ A ready to go [GLIMPSE](https://odelaneau.github.io/GLIMPSE/) docker image.
 Usage:
 
 ```bash
-docker run -it ghcr.io/amanas/docker-glimpse:1.1.1
+docker run -it --name glimpse ghcr.io/amanas/docker-glimpse:1.1.1_v1
 ```
 
 ## Versions
 
+* [samtools](https://github.com/samtools/samtools) 1.14
 * [htslib](http://www.htslib.org/) 1.11
 * [boost](https://www.boost.org/doc/libs/1_73_0/) 1.73.0
 * [bcftools](https://samtools.github.io/bcftools/bcftools.html) 1.9
 * [GLIMPSE](https://odelaneau.github.io/GLIMPSE/installation.html) 1.1.1
+* [Google Cloud SDK](https://cloud.google.com/sdk/docs/install) 364.0.0
 
 ## Build and publish