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fredericlemoinefredericlemoine
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Updated pangolin
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‎pangolin/v4.3.1-v1.21-v0.3.17-v0.1.12/Dockerfile

+11-6
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@@ -1,7 +1,7 @@
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# Largely inspired from
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# https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
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FROM continuumio/miniconda3:23.3.1-0-alpine
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FROM continuumio/miniconda3:23.5.2-0-alpine
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LABEL version="4.3.1" \
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description="Docker image for Pangolin"
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@@ -20,20 +20,25 @@ RUN apk update \
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&& conda update conda \
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&& conda install mamba -c conda-forge
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RUN mamba config --set safety_checks disabled
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RUN cd / \
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&& git clone https://github.com/cov-lineages/pangolin.git \
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&& cd pangolin \
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&& git checkout $VERSION \
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&& cd .. \
30+
&& sed -i 's/snakemake-minimal=/snakemake-minimal>=/' /pangolin/environment.yml \
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&& sed -i 's/pip=19.3.1/pip>=19.3.1/' /pangolin/environment.yml \
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&& sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
33-
&& mamba env update --quiet -f /pangolin/environment.yml && conda clean -a \
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&& cd /pangolin \
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&& pip install . && rm -rf /root/.cache/pip \
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&& pangolin --version &> /pangolin-version.txt
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&& sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml
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#RUN mamba install -y wheel certifi six pycparser jsonpointer charset-normalizer jsonpatch --force-reinstall -c conda-forge \
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# && mamba env update --quiet -f /pangolin/environment.yml && conda clean -a \
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# && cd /pangolin \
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# && pip install . && rm -rf /root/.cache/pip \
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# && pangolin --version &> /pangolin-version.txt
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WORKDIR /tmp/
3944

‎pangolin/v4.3.1-v1.27-v0.3.19-v0.1.12/Dockerfile

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# Largely inspired from
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# https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
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FROM continuumio/miniconda3:23.5.2-0-alpine
5+
LABEL version="4.3.1" \
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description="Docker image for Pangolin"
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ENV VERSION "v4.3.1"
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ENV DATAVERSION "v1.27"
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ENV SCORPIOVERSION "v0.3.19"
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ENV CONSTELLATIONVERSION "v0.1.12"
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# Install git for pangolin
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RUN apk update \
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&& apk add git bash libarchive \
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&& pip install --upgrade pip \
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&& pip uninstall --yes pyOpenSSL \
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&& pip install --upgrade cryptography \
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&& pip install pyOpenSSL \
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&& conda update conda \
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&& conda update --all \
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&& conda install mamba -c conda-forge
23+
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COPY pangolin.patch /
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RUN cd / \
27+
&& git clone https://github.com/cov-lineages/pangolin.git \
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&& cd pangolin \
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&& git checkout $VERSION \
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&& git apply /pangolin.patch \
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&& cd .. \
32+
&& sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
33+
&& sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
34+
&& sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
35+
&& sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
36+
&& sed -i s/pip=.*/pip/ /pangolin/environment.yml \
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&& mamba env update --quiet -f /pangolin/environment.yml && conda clean -a \
38+
&& cd /pangolin \
39+
&& pip install . && rm -rf /root/.cache/pip \
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&& pangolin --version &> /pangolin-version.txt
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WORKDIR /tmp/
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ENTRYPOINT ["pangolin"]

‎pangolin/v4.3.1-v1.27-v0.3.19-v0.1.12/pangolin.patch

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diff --git a/pangolin/scripts/usher.smk b/pangolin/scripts/usher.smk
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index 3adffc7..3ba0938 100644
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--- a/pangolin/scripts/usher.smk
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+++ b/pangolin/scripts/usher.smk
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@@ -106,6 +106,7 @@ rule usher_inference:
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echo ""
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fi
8+
cat {input.fasta:q} >> {params.ref_fa:q}
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+ sed -i 's/^ *//' {params.ref_fa:q}
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faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
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$usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
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else

‎pangolin/v4.3.1-v1.30-v0.3.19-v0.1.12/Dockerfile

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# Largely inspired from
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# https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
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FROM continuumio/miniconda3:23.5.2-0-alpine
5+
LABEL version="4.3.1" \
6+
description="Docker image for Pangolin"
7+
8+
ENV VERSION "v4.3.1"
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ENV DATAVERSION "v1.30"
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ENV SCORPIOVERSION "v0.3.19"
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ENV CONSTELLATIONVERSION "v0.1.12"
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# Install git for pangolin
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RUN apk update \
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&& apk add git bash libarchive \
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&& pip install --upgrade pip \
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&& pip uninstall --yes pyOpenSSL \
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&& pip install --upgrade cryptography \
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&& pip install pyOpenSSL \
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&& conda update conda \
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&& conda update --all \
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&& conda install mamba -c conda-forge
23+
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COPY pangolin.patch /
25+
26+
RUN cd / \
27+
&& git clone https://github.com/cov-lineages/pangolin.git \
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&& cd pangolin \
29+
&& git checkout $VERSION \
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&& git apply /pangolin.patch \
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&& cd .. \
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&& sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
34+
&& sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
36+
&& sed -i s/pip=.*/pip/ /pangolin/environment.yml \
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&& mamba env update --quiet -f /pangolin/environment.yml && conda clean -a \
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&& cd /pangolin \
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&& pip install . && rm -rf /root/.cache/pip \
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&& pangolin --version &> /pangolin-version.txt
41+
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WORKDIR /tmp/
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ENTRYPOINT ["pangolin"]

‎pangolin/v4.3.1-v1.30-v0.3.19-v0.1.12/pangolin.patch

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diff --git a/pangolin/scripts/usher.smk b/pangolin/scripts/usher.smk
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index 3adffc7..3ba0938 100644
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--- a/pangolin/scripts/usher.smk
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+++ b/pangolin/scripts/usher.smk
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@@ -106,6 +106,7 @@ rule usher_inference:
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echo ""
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fi
8+
cat {input.fasta:q} >> {params.ref_fa:q}
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+ sed -i 's/^ *//' {params.ref_fa:q}
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faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
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$usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
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else

‎pangolin/v4.3.1-v1.31-v0.3.19-v0.1.12/Dockerfile

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# Largely inspired from
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# https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
3+
4+
FROM continuumio/miniconda3:23.5.2-0-alpine
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LABEL version="4.3.1" \
6+
description="Docker image for Pangolin"
7+
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ENV VERSION "v4.3.1"
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ENV DATAVERSION "v1.31"
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ENV SCORPIOVERSION "v0.3.19"
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ENV CONSTELLATIONVERSION "v0.1.12"
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# Install git for pangolin
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RUN apk update \
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&& apk add git bash libarchive \
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&& pip install --upgrade pip \
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&& pip uninstall --yes pyOpenSSL \
18+
&& pip install --upgrade cryptography \
19+
&& pip install pyOpenSSL \
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&& conda update conda \
21+
&& conda update --all \
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&& conda install mamba -c conda-forge
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COPY pangolin.patch /
25+
26+
RUN cd / \
27+
&& git clone https://github.com/cov-lineages/pangolin.git \
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&& cd pangolin \
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&& git checkout $VERSION \
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&& git apply /pangolin.patch \
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&& cd .. \
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&& sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
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&& sed -i s/pip=.*/pip/ /pangolin/environment.yml \
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&& mamba env update --quiet -f /pangolin/environment.yml && conda clean -a \
38+
&& cd /pangolin \
39+
&& pip install . && rm -rf /root/.cache/pip \
40+
&& pangolin --version &> /pangolin-version.txt
41+
42+
WORKDIR /tmp/
43+
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ENTRYPOINT ["pangolin"]

‎pangolin/v4.3.1-v1.31-v0.3.19-v0.1.12/pangolin.patch

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diff --git a/pangolin/scripts/usher.smk b/pangolin/scripts/usher.smk
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index 3adffc7..3ba0938 100644
3+
--- a/pangolin/scripts/usher.smk
4+
+++ b/pangolin/scripts/usher.smk
5+
@@ -106,6 +106,7 @@ rule usher_inference:
6+
echo ""
7+
fi
8+
cat {input.fasta:q} >> {params.ref_fa:q}
9+
+ sed -i 's/^ *//' {params.ref_fa:q}
10+
faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
11+
$usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
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else

‎pangolin/v4.3.1-v1.32-v0.3.19-v0.1.12/Dockerfile

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# Largely inspired from
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# https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
3+
4+
FROM continuumio/miniconda3:24.11.1-0
5+
LABEL version="4.3.1" \
6+
description="Docker image for Pangolin"
7+
8+
ENV VERSION "v4.3.1"
9+
ENV DATAVERSION "v1.32"
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ENV SCORPIOVERSION "v0.3.19"
11+
ENV CONSTELLATIONVERSION "v0.1.12"
12+
13+
COPY pangolin.patch /
14+
15+
# Install git for pangolin
16+
RUN apt-get update -y \
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&& apt-get install -y git bash libarchive-dev \
18+
&& pip install --upgrade pip \
19+
&& pip uninstall --yes pyOpenSSL \
20+
&& pip install --upgrade cryptography \
21+
&& pip install pyOpenSSL \
22+
&& conda update -y conda \
23+
&& conda update -y --all
24+
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RUN cd / \
26+
&& git clone https://github.com/cov-lineages/pangolin.git \
27+
&& cd pangolin \
28+
&& git checkout $VERSION \
29+
&& git apply /pangolin.patch \
30+
&& cd .. \
31+
&& sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
32+
&& sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
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&& sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
35+
&& sed -i s/pip=.*/pip/ /pangolin/environment.yml \
36+
&& conda env update --quiet -f /pangolin/environment.yml && conda clean -a \
37+
&& cd /pangolin \
38+
&& pip install . && rm -rf /root/.cache/pip \
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&& pangolin --version > /pangolin-version.txt
40+
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WORKDIR /tmp/
42+
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ENTRYPOINT ["pangolin"]

‎pangolin/v4.3.1-v1.32-v0.3.19-v0.1.12/pangolin.patch

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diff --git a/pangolin/scripts/usher.smk b/pangolin/scripts/usher.smk
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index 3adffc7..3ba0938 100644
3+
--- a/pangolin/scripts/usher.smk
4+
+++ b/pangolin/scripts/usher.smk
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@@ -106,6 +106,7 @@ rule usher_inference:
6+
echo ""
7+
fi
8+
cat {input.fasta:q} >> {params.ref_fa:q}
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+ sed -i 's/^ *//' {params.ref_fa:q}
10+
faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
11+
$usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
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else

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