mirror of
https://github.com/JHUAPL/meta-simulator.git
synced 2026-01-09 16:17:56 -05:00
88 lines
3.6 KiB
Bash
88 lines
3.6 KiB
Bash
#!/bin/bash
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# **********************************************************************
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# Copyright (C) 2020 Johns Hopkins University Applied Physics Laboratory
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#
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# All Rights Reserved.
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# For any other permission, please contact the Legal Office at JHU/APL.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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# **********************************************************************
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####Define ENV variables
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run_dir=$PWD
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g="$(which python)"
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baseBin=$(dirname ${g})
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src_bin="${run_dir}/src"
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mkdir $src_bin
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CONDA_BASE=$(conda info --base)
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source "$CONDA_BASE/etc/profile.d/conda.sh"
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script_location="$(perl -MCwd=abs_path -le 'print abs_path(shift)' $(which $(basename $0)))"
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##########Install DeepSimulator##########################################
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git clone https://github.com/lykaust15/DeepSimulator.git $src_bin/DeepSimulator
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cd $src_bin/DeepSimulator
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find "$PWD" -name "*download*.sh" -print0 | while read -d $'\0' fn; do sed -Ei "s/source activate/conda activate/g" $fn ; done
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find "$PWD" -name "*install.sh" -print0 | while read -d $'\0' fn; do sed -Ei "s/source activate/conda activate/g" $fn ; done
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find "$PWD" -name "*install.sh" -print0 | while read -d $'\0' fn; do sed -Ei "s/source deactivate/conda deactivate/g" $fn ; done
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echo $PWD
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grep -q "source $CONDA_BASE/etc/profile.d/conda.sh" install.sh
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if [[ $? != 0 ]] ; then
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echo "source $CONDA_BASE/etc/profile.d/conda.sh" | cat - install.sh > temp && mv temp install.sh
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fi
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bash install.sh
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#-> 2. install basecaller
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#--| 2.1 install albacore_2.3.1
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cd base_caller/albacore_2.3.1/
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./download_and_install.sh
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cd ../../
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#--| 2.2 install guppy_3.1.5
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cd base_caller/guppy_3.1.5/
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./download_and_install.sh
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cd ../../
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cd $run_dir
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#######Ont guppy upgrade to 3.4.5########################################
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wget https://americas.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_3.4.5_linux64.tar.gz -P src/
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mkdir $src_bin/DeepSimulator/base_caller/guppy_3.4.5
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tar -xvzf src/ont-guppy-cpu_3.4.5_linux64.tar.gz --directory $src_bin/DeepSimulator/base_caller/guppy_3.4.5
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rm -rf src/ont-guppy-cpu_3.4.5_linux64.tar.gz
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#Enable fast mode (less accurate) for cpu basecalling
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sed -Ei "s/hac/fast/g" $src_bin/DeepSimulator/deep_simulator.sh
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sed -Ei "s/guppy=guppy_3\.[0-9]*\.[0-9]*/guppy=guppy_3\.4\.5/g" $src_bin/DeepSimulator/deep_simulator.sh
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sed -Ei "s/source deactivate/conda deactivate/g" $src_bin/DeepSimulator/deep_simulator.sh
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#Create a new deepsim script that exits early i.e. there is no basecalling. It only makes fast5 files
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cp $src_bin/DeepSimulator/deep_simulator.sh $src_bin/DeepSimulator/deep_simulator_fast5only.sh
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sed -Ei "s/guppy=guppy_3\.[0-9]*\.[0-9]*/exit 1/g" $src_bin/DeepSimulator/deep_simulator_fast5only.sh
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#Symlink the two files into the conda environment bin folder
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ln -sf $src_bin/DeepSimulator/deep_simulator.sh\
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$baseBin/
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ln -sf $src_bin/DeepSimulator/deep_simulator_fast5only.sh\
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$baseBin/
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#because albacore doesnt work in the deepsim install script, redo it
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source activate basecall
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wget https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.3.1-cp36-cp36m-manylinux1_x86_64.whl \
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-P $src_bin/
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pip install $src_bin/ont_albacore-2.3.1-cp36-cp36m-manylinux1_x86_64.whl
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rm $src_bin/*albacore*
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