From 5cc7692df35e7485a61ac6e13489d5a38b444534 Mon Sep 17 00:00:00 2001
From: francois-a <francois@broadinstitute.org>
Date: Mon, 3 Jul 2023 04:34:10 +0000
Subject: [PATCH] Updates for v1.0.8

---
 Dockerfile | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 928b11e..a13771d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
 # Dockerfile for tensorQTL
-FROM nvidia/cuda:11.3.1-cudnn8-runtime-ubuntu20.04
+FROM nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu22.04
 MAINTAINER Francois Aguet
 
 RUN apt-get update && apt-get install -y software-properties-common && \
@@ -27,21 +27,21 @@ RUN apt-get update && apt-get install -y software-properties-common && \
 
 # htslib
 RUN cd /opt && \
-    wget --no-check-certificate https://github.com/samtools/htslib/releases/download/1.15.1/htslib-1.15.1.tar.bz2 && \
-    tar -xf htslib-1.15.1.tar.bz2 && rm htslib-1.15.1.tar.bz2 && cd htslib-1.15.1 && \
+    wget --no-check-certificate https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2 && \
+    tar -xf htslib-1.17.tar.bz2 && rm htslib-1.17.tar.bz2 && cd htslib-1.17 && \
     ./configure --enable-libcurl --enable-s3 --enable-plugins --enable-gcs && \
     make && make install && make clean
 
 # bcftools
 RUN cd /opt && \
-    wget --no-check-certificate https://github.com/samtools/bcftools/releases/download/1.15.1/bcftools-1.15.1.tar.bz2 && \
-    tar -xf bcftools-1.15.1.tar.bz2 && rm bcftools-1.15.1.tar.bz2 && cd bcftools-1.15.1 && \
+    wget --no-check-certificate https://github.com/samtools/bcftools/releases/download/1.17/bcftools-1.17.tar.bz2 && \
+    tar -xf bcftools-1.17.tar.bz2 && rm bcftools-1.17.tar.bz2 && cd bcftools-1.17 && \
     ./configure --with-htslib=system && make && make install && make clean
 
 # install R
 ENV DEBIAN_FRONTEND noninteractive
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
+RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/'
 RUN apt update && apt install -y r-base r-base-dev
 ENV R_LIBS_USER=/opt/R/4.0
 RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager")}; BiocManager::install("qvalue");'
@@ -49,10 +49,11 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) {install.p
 # python modules
 RUN pip3 install --upgrade pip setuptools
 RUN pip3 install numpy pandas scipy
-RUN pip3 install pandas-plink ipython jupyter matplotlib pyarrow torch rpy2 gcsfs
+RUN pip3 install pandas-plink ipython jupyter matplotlib pyarrow torch rpy2 gcsfs Pgenlib>=0.90.1
+RUN pip3 install tensorqtl==1.0.8
 
-RUN cd /opt && \
-    wget https://github.com/broadinstitute/tensorqtl/archive/v1.0.7.tar.gz && \
-    tar -xf v1.0.7.tar.gz && mv tensorqtl-1.0.7 tensorqtl && \
-    rm v1.0.7.tar.gz
-RUN pip3 install /opt/tensorqtl/
+# RUN cd /opt && \
+#     wget https://github.com/broadinstitute/tensorqtl/archive/v1.0.8.tar.gz && \
+#     tar -xf v1.0.8.tar.gz && mv tensorqtl-1.0.8 tensorqtl && \
+#     rm v1.0.8.tar.gz
+# RUN pip3 install /opt/tensorqtl/