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Small fixes for beebop #217

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merged 11 commits into from
Sep 7, 2022
Merged

Small fixes for beebop #217

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13f78e3
change manifest to include microreact.pkl
muppi1993 Aug 26, 2022
9cc2df2
remove condition to prevent UnboundLocalError
muppi1993 Aug 26, 2022
5febc24
add dependencies to setup.py
muppi1993 Aug 31, 2022
70b2d3e
install requirements automatically via pip
muppi1993 Aug 31, 2022
e010568
add mandrake installation
muppi1993 Sep 1, 2022
54888c7
use higher cmake version from pip for mandrake installation
muppi1993 Sep 1, 2022
d9feff9
Update Dockerfile
muppi1993 Sep 1, 2022
8b87fc2
add boost installation
muppi1993 Sep 1, 2022
2cca9af
update Dockerfile
muppi1993 Sep 2, 2022
99fef1e
update Dockerfile
muppi1993 Sep 2, 2022
e79f19a
remove boost installation as now included in mandrake
muppi1993 Sep 6, 2022
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1 change: 1 addition & 0 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
recursive-include scripts *.py
recursive-include PopPUNK/data *.gz
recursive-include PopPUNK/data *.pkl
recursive-include vendor *
recursive-include src *
include CMakeLists.txt
2 changes: 1 addition & 1 deletion PopPUNK/visualise.py
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Expand Up @@ -290,7 +290,7 @@ def generate_visualisations(query_db,
combined_seq = rlist

# Fill in qq-distances if required
if self == False and tree != "none":
if self == False:
sys.stderr.write("Note: Distances in " + distances + " are from assign mode\n"
"Note: Distance will be extended to full all-vs-all distances\n"
"Note: Re-run poppunk_assign with --update-db to avoid this\n")
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14 changes: 9 additions & 5 deletions docker2/Dockerfile
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Expand Up @@ -33,11 +33,15 @@ RUN add-apt-repository https://downloads.skewed.de/apt && \
ln -s /usr/lib/python3/dist-packages/graph_tool \
/usr/local/lib/python3.10/site-packages

COPY requirements.txt /tmp/requirements.txt
RUN pip install pybind11 && \
pip install -r /tmp/requirements.txt && \
rm -f /tmp/requirements.txt
RUN pip install pybind11[global]

COPY . /src
WORKDIR /src
RUN python setup.py install
RUN pip install .

RUN pip install cmake plotly ffmpeg

RUN git clone -b bacpop-49 https://github.com/bacpop/mandrake.git && \
cd mandrake && \
python setup.py install && \
cd .. && rm -r mandrake
13 changes: 13 additions & 0 deletions setup.py
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Expand Up @@ -103,6 +103,19 @@ def build_extension(self, ext):
'Programming Language :: Python :: 3.8',
],
python_requires='>=3.8.0',
install_requires=['biopython',
'h5py',
'hdbscan',
'matplotlib',
# 'mandrake', #uncomment when on PyPI
'networkx',
'pandas',
'pp-sketchlib',
'requests',
'scikit-learn',
'tqdm',
'treeswift',
],
keywords='bacteria genomics population-genetics k-mer',
packages=['PopPUNK'],
entry_points={
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