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requirements.txt
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requirements.txt
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#
# This file is autogenerated by pip-compile with Python 3.12
# by the following command:
#
# pip-compile
#
addict==2.4.0
# via toil
annotated-types==0.7.0
# via pydantic
apache-libcloud==2.8.3
# via toil
argcomplete==3.5.1
# via cwltool
asttokens==2.4.1
# via stack-data
awscli==1.35.16
# via -r requirements.in
biopython==1.84
# via -r requirements.in
bleach==6.1.0
# via galaxy-util
blessed==1.20.0
# via enlighten
boltons==24.0.0
# via galaxy-util
boto3==1.35.50
# via
# boto3-stubs
# moto
boto3-stubs[autoscaling,boto3,ec2,iam,s3,sdb,sts]==1.35.50
# via toil
botocore==1.35.50
# via
# awscli
# boto3
# boto3-stubs
# moto
# s3transfer
botocore-stubs==1.35.50
# via boto3-stubs
build==1.2.2.post1
# via pip-tools
cachecontrol[filecache]==0.14.0
# via
# schema-salad
# toil
cachetools==5.5.0
# via google-auth
certifi==2024.8.30
# via requests
cffi==1.17.1
# via
# cryptography
# pynacl
charset-normalizer==3.4.0
# via requests
click==8.1.7
# via pip-tools
colorama==0.4.6
# via awscli
coloredlogs==15.0.1
# via
# cwltool
# toil
conda-package-streaming==0.11.0
# via galaxy-tool-util
configargparse==1.7
# via toil
contourpy==1.3.0
# via matplotlib
cryptography==43.0.3
# via moto
cwl-upgrader==1.2.11
# via cwl-utils
cwl-utils==0.35
# via cwltool
cwltool==3.1.20240508115724
# via toil
cycler==0.12.1
# via matplotlib
decorator==5.1.1
# via ipython
dill==0.3.9
# via toil
docker==7.1.0
# via toil
docutils==0.16
# via
# awscli
# galaxy-util
ec2-metadata==2.14.0
# via toil
enlighten==1.12.4
# via toil
executing==2.1.0
# via stack-data
filelock==3.16.1
# via cachecontrol
fonttools==4.54.1
# via matplotlib
galaxy-tool-util==24.1.3
# via toil
galaxy-util==24.1.3
# via
# galaxy-tool-util
# toil
google-api-core==2.22.0
# via
# google-cloud-core
# google-cloud-storage
google-auth==2.35.0
# via
# google-api-core
# google-cloud-core
# google-cloud-storage
# toil
google-cloud-core==2.4.1
# via google-cloud-storage
google-cloud-storage==2.8.0
# via toil
google-crc32c==1.6.0
# via google-resumable-media
google-resumable-media==2.7.2
# via google-cloud-storage
googleapis-common-protos==1.65.0
# via google-api-core
humanfriendly==10.0
# via coloredlogs
idna==3.10
# via requests
ipython==8.29.0
# via -r requirements.in
isodate==0.6.1
# via rdflib
jedi==0.19.1
# via ipython
jinja2==3.1.4
# via moto
jmespath==1.0.1
# via
# boto3
# botocore
joblib==1.4.2
# via scikit-learn
kiwisolver==1.4.7
# via matplotlib
lxml==5.3.0
# via
# galaxy-tool-util
# prov
markupsafe==3.0.2
# via
# galaxy-tool-util
# jinja2
# werkzeug
matplotlib==3.9.2
# via -r requirements.in
matplotlib-inline==0.1.7
# via ipython
mistune==3.0.2
# via schema-salad
moto==5.0.18
# via toil
msgpack==1.1.0
# via cachecontrol
mypy-boto3-autoscaling==1.35.45
# via boto3-stubs
mypy-boto3-ec2==1.35.48
# via boto3-stubs
mypy-boto3-iam==1.35.0
# via
# boto3-stubs
# toil
mypy-boto3-s3==1.35.46
# via
# boto3-stubs
# toil
mypy-boto3-sdb==1.35.0
# via boto3-stubs
mypy-boto3-sts==1.35.0
# via boto3-stubs
mypy-extensions==1.0.0
# via
# cwltool
# schema-salad
networkx==3.4.2
# via
# prov
# toil
numpy==2.1.2
# via
# biopython
# contourpy
# matplotlib
# scikit-learn
# scipy
packaging==24.1
# via
# build
# cwl-utils
# galaxy-tool-util
# galaxy-util
# matplotlib
parso==0.8.4
# via jedi
pexpect==4.9.0
# via ipython
pillow==11.0.0
# via matplotlib
pip-tools==7.4.1
# via -r requirements.in
prefixed==0.9.0
# via enlighten
prompt-toolkit==3.0.48
# via ipython
proto-plus==1.25.0
# via google-api-core
protobuf==5.28.3
# via
# google-api-core
# googleapis-common-protos
# proto-plus
prov==1.5.1
# via cwltool
psutil==5.9.8
# via
# cwltool
# toil
ptyprocess==0.7.0
# via pexpect
pure-eval==0.2.3
# via stack-data
pyasn1==0.6.1
# via
# pyasn1-modules
# rsa
pyasn1-modules==0.4.1
# via google-auth
pycparser==2.22
# via cffi
pydantic==2.9.2
# via galaxy-tool-util
pydantic-core==2.23.4
# via pydantic
pydot==3.0.2
# via cwltool
pygments==2.18.0
# via ipython
pynacl==1.5.0
# via toil
pyparsing==3.2.0
# via
# cwltool
# galaxy-util
# matplotlib
# pydot
# rdflib
pyproject-hooks==1.2.0
# via
# build
# pip-tools
pypubsub==4.0.3
# via toil
python-dateutil==2.9.0.post0
# via
# botocore
# matplotlib
# moto
# prov
# toil
pyyaml==6.0.2
# via
# awscli
# galaxy-tool-util
# galaxy-util
# responses
# toil
rdflib==7.0.0
# via
# cwl-utils
# cwltool
# prov
# schema-salad
repoze-lru==0.7
# via routes
requests==2.31.0
# via
# apache-libcloud
# cachecontrol
# conda-package-streaming
# cwl-utils
# cwltool
# docker
# ec2-metadata
# galaxy-tool-util
# galaxy-util
# google-api-core
# google-cloud-storage
# moto
# responses
# schema-salad
# toil
responses==0.25.3
# via moto
routes==2.5.1
# via galaxy-util
rsa==4.7.2
# via
# awscli
# google-auth
ruamel-yaml==0.18.6
# via
# cwl-upgrader
# cwl-utils
# cwltool
# schema-salad
# toil
ruamel-yaml-clib==0.2.12
# via
# ruamel-yaml
# toil
s3transfer==0.10.3
# via
# awscli
# boto3
schema-salad==8.7.20241021092521
# via
# cwl-upgrader
# cwl-utils
# cwltool
# toil
scikit-learn==1.5.2
# via -r requirements.in
scipy==1.14.1
# via scikit-learn
shellescape==3.8.1
# via cwltool
six==1.16.0
# via
# asttokens
# bleach
# blessed
# isodate
# prov
# python-dateutil
# routes
sortedcontainers==2.4.0
# via galaxy-tool-util
spython==0.3.14
# via cwltool
stack-data==0.6.3
# via ipython
threadpoolctl==3.5.0
# via scikit-learn
toil[aws,cwl,encryption,google,mesos]==7.0.0
# via -r requirements.in
traitlets==5.14.3
# via
# ipython
# matplotlib-inline
types-awscrt==0.23.0
# via botocore-stubs
types-s3transfer==0.10.3
# via boto3-stubs
typing-extensions==4.12.2
# via
# galaxy-tool-util
# galaxy-util
# pydantic
# pydantic-core
# toil
urllib3==2.2.3
# via
# botocore
# docker
# requests
# responses
# toil
wcwidth==0.2.13
# via
# blessed
# prompt-toolkit
webencodings==0.5.1
# via bleach
werkzeug==3.0.6
# via moto
wheel==0.44.0
# via pip-tools
xmltodict==0.14.2
# via moto
zipstream-new==1.1.8
# via galaxy-util
zstandard==0.23.0
# via conda-package-streaming
# The following packages are considered to be unsafe in a requirements file:
# pip
# setuptools