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Updates needed for rebuilding docker image #10

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2 changes: 1 addition & 1 deletion .gitmodules
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[submodule "miqScoreNGSReadCountPublic"]
path = miqScoreNGSReadCountPublic
url = git@github.com:Zymo-Research/miqScoreNGSReadCountPublic.git
url = https://github.com/Zymo-Research/miqScoreNGSReadCountPublic.git
[submodule "miqScoreShotgunPublicSupport"]
path = miqScoreShotgunPublicSupport
url = https://github.com/Zymo-Research/miqScoreShotgunPublicSupport.git
7 changes: 5 additions & 2 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM python:3.6.7
FROM python:3.7

MAINTAINER Michael M. Weinstein, Zymo Research
LABEL version="0.0.1"
Expand All @@ -7,6 +7,8 @@ WORKDIR /

RUN apt-get update && \
apt install -y autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libssl-dev libncurses5-dev && \
apt autoclean && \
apt autoremove -y && \
cd tmp && \
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && \
tar -xjvf samtools-1.9.tar.bz2 && \
Expand All @@ -27,7 +29,7 @@ RUN cd /tmp &&\
tar -xvf v0.7.16.tar.gz && \
rm v0.7.16.tar.gz && \
cd bwa-0.7.16 &&\
make && \
make CC='gcc -fcommon' && \
cd /tmp && \
cp -r bwa-0.7.16 /opt/ && \
rm -rf bwa-0.7.16
Expand Down Expand Up @@ -61,6 +63,7 @@ COPY ./requirements.txt /opt/referenceBuild

#doing expensive and unlikely to change build processes here to speed up testing builds
RUN cd /opt/referenceBuild/ && \
pip3 install -U pip && \
pip3 install -r requirements.txt && \
cd reference && \
echo "Indexing standard genome" && \
Expand Down
6 changes: 3 additions & 3 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
numpy==1.13.1
scipy==1.2.1
matplotlib==3.0.2
numpy==1.17.0
scipy==1.7.3
matplotlib==3.5
pysam==0.15.3