From 28da9a6d4145e780b88f90d7a3fc6a31b57ff7b3 Mon Sep 17 00:00:00 2001
From: subwaystation <simon.heumos@qbic.uni-tuebingen.de>
Date: Wed, 13 Mar 2024 10:34:04 +0100
Subject: [PATCH] multiqc 1.21, bcftools 1.19

---
 Dockerfile | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 8343c47..641fdcc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -32,7 +32,6 @@ RUN apt-get update \
                        curl \
                        pigz \
                        tabix \
-                       bcftools \
                        samtools \
                        wget \
                        pip \
@@ -97,7 +96,7 @@ RUN git clone https://github.com/marschall-lab/GFAffix.git \
     && cd ../ \
     && rm -rf GFAffix
 
-RUN pip install multiqc==1.18
+RUN pip install multiqc==1.21
 
 RUN wget https://github.com/vgteam/vg/releases/download/v1.40.0/vg && chmod +x vg && mv vg /usr/local/bin/vg
 
@@ -178,6 +177,11 @@ RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.s
     && mv bedtools.static /usr/local/bin/bedtools \
     && chmod +x /usr/local/bin/bedtools
 
+# current bcftools
+RUN wget https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2 \
+    && tar xjf bcftools-1.19.tar.bz2 \
+    && bcftools-1.19/ && ./configure --prefix=/usr/local/bin/ && make && make install && export PATH=/usr/local/bin/bin:$PATH
+
 # copy required scripts
 COPY scripts/* /usr/local/bin/
 COPY scripts /usr/local/bin/scripts/