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MANIFEST.in
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MANIFEST.in
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# MANIFEST.in
#
# This tells setuptools what files to distribute.
include MANIFEST.in
include requirements.txt
include requirements-ext.txt
include *.rst
include .zenodo.json
include .flake8
recursive-include thapbi_pict *.py
recursive-include scripts *.py
include scripts/README.rst
# Placing the DB binary file within the Python tree as
# the simplest way to get it included in a wheel for install:
include thapbi_pict/ITS1_DB.sqlite
# Deliberately not risking everything in database/ via wildcards.
# e.g. NCBI taxonomy or symlinks to control plate positive controls.
include database/README.rst
include database/ITS1_DB.fasta
include database/build_ITS1_DB.sh
include database/controls.fasta
include database/Phytophthora_ITS1_curated.fasta
include database/Nothophytophthora_ITS1_curated.fasta
include database/Oomycota_ITS1_w32.fasta
include database/Oomycota_ITS1_obs.fasta
include database/single_isolates/*.fasta
# The following is better than a blanket include wildcard * but
# this still risks unwanted includes of any working files:
recursive-include tests *.sh *.rst *.tsv *.fasta *.fastq.gz *.xgmml
include tests/reads/6e847180a4da6eed316e1fb98b21218f_R?.fastq
include tests/reads/SRR6303948_sample_?.fastq
include tests/reads/*.md5
include tests/woody_hosts/intermediate.tar.bz2
prune tests/woody_hosts/raw_data/
prune tests/woody_hosts/positive_controls/
prune tests/woody_hosts/summary/
prune tests/woody_hosts/intermediate/
prune examples/
include examples/README.rst
include examples/woody_hosts/README.rst
include examples/woody_hosts/metadata.tsv
include examples/woody_hosts/setup.sh
include examples/woody_hosts/run.sh
include examples/woody_hosts/intermediate.tar.bz2
include examples/woody_hosts/expected/*.known.tsv
include examples/recycled_water/README.rst
include examples/recycled_water/PRJNA417859.tsv
include examples/recycled_water/setup.sh
include examples/recycled_water/run.sh
include examples/recycled_water/Redekar_et_al_2019_sup_table_3.fasta
include examples/recycled_water/Redekar_et_al_2019_sup_table_3.tsv
include examples/recycled_water/make_meta.py
include examples/recycled_water/metadata.tsv
include examples/recycled_water/raw_data/MD5SUM.txt
include examples/fungal_mock/README.rst
include examples/fungal_mock/PRJNA377530.tsv
include examples/fungal_mock/ITS1.fasta
include examples/fungal_mock/ITS2.fasta
include examples/fungal_mock/mock_community.known.tsv
include examples/fungal_mock/negative_control.known.tsv
include examples/fungal_mock/setup.sh
include examples/fungal_mock/run.sh
include examples/fungal_mock/metadata_AL1.tsv
include examples/fungal_mock/metadata_AL2.tsv
include examples/fungal_mock/raw_data/AL2/MD5SUM.txt
include examples/fungal_mock/raw_data/AL2/MD5SUM.txt
include examples/great_lakes/README.rst
include examples/great_lakes/PRJNA379165.tsv
include examples/great_lakes/setup.sh
include examples/great_lakes/run.sh
include examples/great_lakes/metadata.tsv
include examples/great_lakes/MOL16S.fasta
include examples/great_lakes/SPH16S.fasta
include examples/great_lakes/raw_data/MD5SUM.txt
include examples/great_lakes/expected/mock_community.MOL16S.known.tsv
include examples/great_lakes/expected/mock_community.SPH16S.known.tsv
include examples/great_lakes/expected/negative_control.known.tsv
include examples/fecal_sequel/README.rst
include examples/fecal_sequel/PRJNA574765.tsv
include examples/fecal_sequel/setup.sh
include examples/fecal_sequel/run.sh
include examples/fecal_sequel/metadata.tsv
include examples/fecal_sequel/curated_bats.fasta
include examples/fecal_sequel/observed_3_bats.fasta
include examples/fecal_sequel/mock_community.known.tsv
include examples/fecal_sequel/raw_data/MD5SUM.txt
include examples/soil_nematodes/README.rst
include examples/soil_nematodes/PRJEB27581.tsv
include examples/soil_nematodes/setup.sh
include examples/soil_nematodes/run.sh
include examples/soil_nematodes/metadata.tsv
include examples/soil_nematodes/mock_community.known.tsv
include examples/soil_nematodes/negative_control.known.tsv
include examples/soil_nematodes/raw_data/MD5SUM.txt
include examples/endangered_species/README.rst
include examples/endangered_species/PRJEB18620.tsv
include examples/endangered_species/setup.sh
include examples/endangered_species/run.sh
include examples/endangered_species/metadata.tsv
include examples/endangered_species/raw_download/MD5SUM.txt
include examples/endangered_species/expected/EM_*.known.tsv
include examples/endangered_species/expected/S*.template.tsv
include examples/endangered_species/references/*.fasta