20765: Adding gvcf regions subdir.

[lightning.git] / docker / vcfutil / Dockerfile

diff --git a/docker/vcfutil/Dockerfile b/docker/vcfutil/Dockerfile
index d3427b74ecd15f65bbada347b6491580f94c7684..38cdedb80961f2a7290290c22731d3991584a4a8 100644 (file)
--- a/docker/vcfutil/Dockerfile
+++ b/docker/vcfutil/Dockerfile
@@ -2,8 +2,11 @@
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-FROM arvados/jobs
-MAINTAINER Jiayong Li <jli@curii.com>
+# build instruction:
+# docker build -t dockername --file=/path/to/lightning/docker/vcfutil/Dockerfile /path/to/lightning
+
+
+FROM python:3.11-buster
 
 USER root
 
@@ -12,6 +15,9 @@ RUN apt-get update -q
 RUN apt-get install -qy build-essential wget cmake zlib1g-dev \
     libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev git vcftools
 
+# Setting up gvcf_region
+COPY ./gvcf_regions /gvcf_regions
+
 # Getting HTSLIB 1.9 for tabix/bgzip
 
 RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar -xjvf htslib-1.9.tar.bz2 && \
@@ -58,9 +64,3 @@ WORKDIR /
 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz && \
     tar -xzvf bedtools-2.27.1.tar.gz && \
     cd bedtools2 && make && cp bin/* /usr/local/bin
-
-WORKDIR /
-
-# Installing gvcf_regions
-
-RUN git clone https://github.com/lijiayong/gvcf_regions