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Add GenoFLU dependencies #243

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Feb 20, 2025
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Add GenoFLU dependencies #243

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5 changes: 5 additions & 0 deletions Dockerfile
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Expand Up @@ -259,6 +259,9 @@ RUN pip3 install pango_aliasor==0.3.0
RUN pip3 install pathogen-embed==3.0.0
RUN pip3 install xlrd==2.0.1

# Install openpyxl for pandas in GenoFLU
RUN pip3 install openpyxl==3.1.0

# 2. Add unpinned programs

# Allow caching to be avoided from here on out in this stage by calling
Expand Down Expand Up @@ -309,6 +312,7 @@ SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]
# less: for usability in an interactive prompt
# libgomp1: for running FastTree
# libsqlite3: for pyfastx (for Augur)
# ncbi-blast+: for GenoFLU in avian-flu
# perl: for running VCFtools
# ruby: may be used by workflows
# sqlite3: for `augur merge`
Expand All @@ -326,6 +330,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
less \
libgomp1 \
libsqlite3-0 \
ncbi-blast+ \
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Ah, just caught up on conversation in #127.

Worth noting this is installing https://packages.debian.org/bookworm/ncbi-blast+ which is v2.12.0.

perl \
ruby \
sqlite3 \
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