galaxy

https://github.com/thesarkis/galaxy

Science Score: 18.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
○
codemeta.json file
○
.zenodo.json file
○
DOI references
○
Academic publication links
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: thesarkis
License: other
Language: Python
Default Branch: master
Size: 435 MB

Statistics

Stars: 0
Watchers: 0
Forks: 0
Open Issues: 41
Releases: 0

Created over 7 years ago · Last pushed over 3 years ago

Metadata Files

Readme Contributing License Code of conduct Citation Security

README.rst

.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
   :alt: Galaxy Logo

The latest information about Galaxy is available via `https://galaxyproject.org/ `__

.. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg
    :target: https://biostar.usegalaxy.org
    :alt: Ask a question

.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
    :target: https://webchat.freenode.net/?channels=galaxyproject
    :alt: Chat on irc

.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
    :target: https://gitter.im/galaxyproject/Lobby
    :alt: Chat on gitter

.. image:: https://img.shields.io/badge/release-documentation-blue.svg
    :target: https://docs.galaxyproject.org/en/master/
    :alt: Release Documentation

.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
    :target: https://travis-ci.org/galaxyproject/galaxy
    :alt: Inspect the test results

Galaxy Quickstart
=================

Galaxy requires Python 2.7 To check your python version, run:

.. code:: console

    $ python -V
    Python 2.7.3

Start Galaxy:

.. code:: console

    $ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your
browser at:

http://localhost:8080

Configuration & Tools
=====================

You may wish to make changes from the default configuration. This can be
done in the ``config/galaxy.ini`` file.

Tools can be either installed from the Tool Shed or added manually.
 For details please see the `tutorial `__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.

Issues and Galaxy Development
=============================

Please see `CONTRIBUTING.md `_ .

Roadmap
=============================

Interested in the next steps for Galaxy? Take a look at the `roadmap `__.

Owner

Login: thesarkis
Kind: user

Repositories: 1
Profile: https://github.com/thesarkis

Citation (CITATION)

If you use or extend Galaxy in your published work, please cite this
publication:

- Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton
  J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson
  J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks
  J. "The Galaxy platform for accessible, reproducible and collaborative
  biomedical analyses: 2016 update"
  Nucleic Acids Research (2016) 44(W1):W3-W10 doi:10.1093/nar/gkw343

BibTeX format:

@article{afgan2016galaxy,
  title={The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2016 update},
  author={Afgan, Enis and Baker, Dannon and van den Beek, Marius and Blankenberg, Daniel and Bouvier, Dave and \v{C}ech, Martin and Chilton, John and Clements, Dave and Coraor, Nate and Eberhard, Carl and Gr\"uning, Bj\"orn and Guerler, Aysam and Hillman-Jackson, Jennifer and Von Kuster, Greg and Rasche, Eric and Soranzo, Nicola and Turaga, Nitesh and Taylor, James and Nekrutenko, Anton and Goecks, Jeremy},
  journal={Nucleic Acids Res.},
  volume={44},
  number={W1},
  pages={W3-W10},
  year={2016},
  publisher={Oxford University Press}
}


More publications
-----------------

To cite specific Galaxy components/features or other Galaxy project
publications, see

https://galaxyproject.org/citing-galaxy

GitHub Events

Total

Last Year

Dependencies

client/bower.json bower

dynatree ~1.2.5
farbtastic ~2.0.0-alpha.1
jStorage ~0.4.12
jquery-autocomplete git://github.com/dyve/jquery-autocomplete
jquery-form ~3.46.0
jquery-ui git://github.com/jquery/jquery-ui.git#~1.11.2
jstree ~3.0.9
select2 ~3.5.2
threedubmedia.jquery.event *
toastr ~2.1.0
wymeditor ~1.0.0-rc.1

client/package.json npm

babel-core ^6.24.0 development
babel-loader ^7.1.1 development
babel-plugin-transform-inline-environment-variables ^0.4.0 development
babel-plugin-transform-vue-template ^0.3.1 development
babel-preset-env ^1.6.1 development
chai ^4.1.2 development
concurrently ^3.5.1 development
css-loader ^0.28.7 development
del ^3.0.0 development
expose-loader ^0.7.4 development
grunt ^0.4.5 development
grunt-cli ^0.1.13 development
grunt-spritesmith ^4.7.1 development
gulp ^3.9.1 development
gulp-babel ^7.0.0 development
gulp-beautify ^2.0.1 development
gulp-cached ^1.1.1 development
gulp-if ^2.0.2 development
gulp-plumber ^1.1.0 development
gulp-sourcemaps ^2.5.1 development
gulp-uglify ^3.0.0 development
gulp-watch ^4.3.11 development
jshint ^2.9.4 development
karma ^1.7.1 development
karma-mocha ^1.3.0 development
karma-phantomjs-launcher ^1.0.4 development
karma-polyfill ^1.0.0 development
karma-qunit ^1.2.1 development
karma-webpack ^2.0.6 development
mocha ^5.0.5 development
node-sass ^4.8.3 development
phantomjs-polyfill 0.0.2 development
phantomjs-prebuilt ^2.1.7 development
prettier ^1.11.1 development
qunitjs ^2.4.1 development
sass-loader ^6.0.7 development
sinon ^4.1.2 development
vue-loader ^14.2.2 development
vue-styleguidist ^1.6.1 development
vue-template-compiler 2.5.16 development
webpack ^3.10.0 development
yaml-loader ^0.5.0 development
@handsontable/vue ^2.0.0-beta1
amdi18n-loader ^0.6.1
axios ^0.17.0
backbone 1.3
bibtex-parse-js ^0.0.24
bootstrap ^4.1.1
bootstrap-tour https://github.com/sorich87/bootstrap-tour.git#6a1028fb562f9aa68c451f0901f8cfeb43cad140
bootstrap-vue ^2.0.0-rc.8
d3 3
font-awesome ^4.7.0
gulp-sass ^3.1.0
handsontable ^2.0.0
jquery 2
jquery-migrate ~1.4
jquery-mousewheel ^3.1.13
jquery-ui-bundle ^1.12.1
jquery.complexify ^0.5.2
jquery.cookie ^1.4.1
latex-parser ^0.6.2
latex-to-unicode-converter ^0.5.0
popper.js ^1.14.3
pyre-to-regexp ^0.0.5
raven-js ^3.17.0
requirejs 2
underscore ^1.8.3
vue 2.5.16

client/yarn.lock npm

1736 dependencies

config/plugins/visualizations/cytoscape/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
cytoscape ^3.2.8
jquery ^3.1.1
parcel-bundler ^1.4.1

config/plugins/visualizations/drawrna/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
drawrnajs ^1.2.6
jquery ^3.1.1
parcel-bundler ^1.4.1

config/plugins/visualizations/example/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
d3 ^4.12.2
jquery ^3.1.1
parcel-bundler ^1.4.1
underscore ^1.8.3

config/plugins/visualizations/heatmap/heatmap_default/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
d3 3
jquery ^3.1.1
parcel-bundler ^1.4.1

config/plugins/visualizations/jqplot/jqplot_bar/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
d3 ^4.12.2
jqplot-exported ^1.0.9-pm.9
jquery ^3.1.1
parcel-bundler ^1.4.1

config/plugins/visualizations/msa/package.json npm

babel-plugin-transform-export-extensions ^6.22.0
babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
es2015 0.0.0
jquery ^3.1.1
msa ^1.0.3
parcel-bundler ^1.4.1

config/plugins/visualizations/ngl/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
jquery ^3.1.1
ngl ^0.10.4
parcel-bundler ^1.4.1

config/plugins/visualizations/nvd3/nvd3_bar/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
d3 ^3.4.5
jquery ^3.3.1
nvd3 ^1.8.6
parcel-bundler ^1.4.1
underscore ^1.8.3

config/plugins/visualizations/phylocanvas/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
jquery ^3.1.1
parcel-bundler ^1.4.1
phylocanvas ^2.8.1

config/plugins/visualizations/pv/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bio-pv ^1.8.1
bootstrap ^3.3.7
jquery ^3.1.1
parcel-bundler ^1.4.1

config/plugins/visualizations/scatterplot/package.json npm

babel-plugin-auto-import ^0.7.1
babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
d3 ^3.5.17
jquery ^3.2.1
jquery-ui-bundle ^1.12.1-migrate
parcel-bundler ^1.6.2
underscore ^1.8.3

config/plugins/visualizations/venn/package.json npm

babel-preset-env ^1.6.1
backbone ^1.3.3
bootstrap ^3.3.7
d3 ^3.4.5
jquery ^3.1.1
parcel-bundler ^1.4.1

lib/galaxy/web/proxy/js/package.json npm

commander ~2.14.1
eventemitter3 0.1.6
http-proxy 1.16.2
sqlite3 3.1.13

lib/galaxy/dependencies/conditional-requirements.txt pypi

MySQL-python *
Pygments ==2.2.0
WebError ==0.10.3
azure-storage ==0.32.0
chronos-python ==0.38.0
cloudbridge ==0.3.3
docker *
drmaa *
fluent-logger *
graphitesend *
kamaki *
pbs_python *
psycopg2-binary ==2.7.4
python-ldap ==2.4.44
python-openid *
python-pam *
raven *
statsd *
watchdog *

lib/galaxy/dependencies/dev-requirements.txt pypi

alabaster ==0.7.10 development
argh ==0.26.2 development
babel ==2.5.3 development
certifi ==2018.1.18 development
chardet ==3.0.4 development
commonmark ==0.5.4 development
docutils ==0.14 development
funcsigs ==1.0.2 development
idna ==2.6 development
imagesize ==1.0.0 development
jinja2 ==2.10 development
lxml ==4.2.1 development
markupsafe ==1.0 development
mock ==2.0.0 development
nodeenv ==1.3.0 development
nose ==1.3.7 development
nosehtml ==0.4.4 development
packaging ==17.1 development
pathtools ==0.1.2 development
pbr ==4.0.2 development
pygithub3 ==0.5.1 development
pygments ==2.2.0 development
pyparsing ==2.2.0 development
pytz ==2018.4 development
pyyaml ==3.12 development
recommonmark ==0.4.0 development
requests ==2.18.4 development
selenium ==3.11.0 development
six ==1.11.0 development
snowballstemmer ==1.2.1 development
sphinx ==1.6.7 development
sphinx-rtd-theme ==0.3.0 development
sphinxcontrib-websupport ==1.0.1 development
testfixtures ==6.0.0 development
twill ==0.9.1 development
typing ==3.6.4 development
urllib3 ==1.22 development
watchdog ==0.8.3 development

lib/galaxy/dependencies/pinned-requirements.txt pypi

amqp ==2.2.2
appdirs ==1.4.3
asn1crypto ==0.24.0
babel ==2.5.3
bagit ==1.6.4
bcrypt ==3.1.4
bdbag ==1.2.4
beaker ==1.9.1
bioblend ==0.10.0
bleach ==2.1.3
boltons ==18.0.0
boto ==2.46.1
bunch ==1.0.1
bx-python ==0.8.1
bz2file ==0.98
certifi ==2018.1.18
cffi ==1.11.5
chardet ==3.0.4
cheetah3 ==3.1.0
cliff ==2.11.0
cloudbridge ==0.3.3
cmd2 ==0.8.4
contextlib2 ==0.5.5
cryptography ==2.2.2
debtcollector ==1.19.0
decorator ==4.2.1
deprecation ==2.0.1
dictobj ==0.4
docopt ==0.6.2
docutils ==0.14
dogpile.cache ==0.6.5
enum34 ==1.1.6
fabric3 ==1.14.post1
funcsigs ==1.0.2
functools32 ==3.2.3.post2
future ==0.16.0
futures ==3.2.0
galaxy-sequence-utils ==1.1.2
globus-sdk ==1.3.0
h5py ==2.6.0
html5lib ==1.0.1
idna ==2.6
ipaddress ==1.0.19
iso8601 ==0.1.12
jmespath ==0.9.3
jsonpatch ==1.23
jsonpointer ==2.0
jsonschema ==2.6.0
keystoneauth1 ==3.4.0
kombu ==4.1.0
mako ==1.0.7
markupsafe ==1.0
mercurial ==3.7.3
monotonic ==1.4
msgpack ==0.5.6
munch ==2.3.1
netaddr ==0.7.19
netifaces ==0.10.6
nose ==1.3.7
numpy ==1.14.2
oauthlib ==2.0.7
openstacksdk ==0.12.0
os-client-config ==1.29.0
os-service-types ==1.2.0
osc-lib ==1.10.0
oslo.config ==6.0.2
oslo.i18n ==3.20.0
oslo.serialization ==2.25.0
oslo.utils ==3.36.0
packaging ==17.1
paramiko ==2.4.1
parsley ==1.3
paste ==2.0.3
pastedeploy ==1.5.2
pastescript ==2.0.2
pbr ==4.0.2
positional ==1.2.1
prettytable ==0.7.2
psutil ==5.4.3
pulsar-galaxy-lib ==0.8.3
py2-ipaddress ==3.4.1
pyasn1 ==0.4.2
pycparser ==2.18
pycrypto ==2.6.1
pycryptodomex ==3.6.0
pyjwkest ==1.4.0
pyjwt ==1.6.1
pykwalify ==1.6.1
pynacl ==1.2.1
pyparsing ==2.2.0
pyperclip ==1.6.0
pysam ==0.14.1
python-cinderclient ==2.0.1
python-dateutil ==2.7.2
python-genomespaceclient ==0.2
python-glanceclient ==2.6.0
python-keystoneclient ==3.10.0
python-lzo ==1.11
python-neutronclient ==6.1.0
python-novaclient ==7.0.0
python-openid ==2.2.5
python-swiftclient ==3.3.0
pytz ==2018.4
pyyaml ==3.12
repoze.lru ==0.7
requests ==2.18.4
requests-oauthlib ==0.8.0
requests-toolbelt ==0.8.0
requestsexceptions ==1.4.0
retrying ==1.3.3
rfc3986 ==1.1.0
routes ==2.4.1
simplejson ==3.13.2
six ==1.11.0
social-auth-core ==1.5.0
sqlalchemy ==1.2.6
sqlalchemy-migrate ==0.11.0
sqlalchemy-utils ==0.33.2
sqlparse ==0.2.4
stevedore ==1.28.0
subprocess32 ==3.5.0
svgwrite ==1.1.12
tempita ==0.5.2
tzlocal ==1.5.1
unicodecsv ==0.14.1
urllib3 ==1.22
uwsgi ==2.0.17
vine ==1.1.4
warlock ==1.2.0
wcwidth ==0.1.7
webencodings ==0.5.1
webob ==1.4.2
whoosh ==2.7.4
wrapt ==1.10.11

lib/galaxy/dependencies/pipfiles/default/Pipfile pypi

Babel *
Beaker *
Cheetah3 *
Fabric3 *
Mako *
MarkupSafe *
Mercurial <=3.7.3
Parsley *
Paste *
PyYAML *
Routes *
SQLAlchemy *
SQLAlchemy-Utils *
WebOb <=1.4.2
Whoosh *
bdbag *
bioblend *
bleach *
boltons *
boto *
bx-python *
bz2file *
dictobj *
docutils *
galaxy_sequence_utils *
h5py !=2.7.0, !=2.7.1
ipaddress *
kombu *
nose *
numpy *
paramiko *
psutil *
pulsar-galaxy-lib *
pycrypto *
pykwalify *
pyparsing *
pysam ==0.14.1
python-genomespaceclient <1.0
requests *
six *
social_auth_core ==1.5.0
sqlalchemy-migrate *
sqlparse *
svgwrite *
uWSGI *

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt pypi

amqp ==2.2.2
appdirs ==1.4.3
asn1crypto ==0.24.0
babel ==2.5.3
bagit ==1.6.4
bcrypt ==3.1.4
bdbag ==1.2.4
beaker ==1.9.1
bioblend ==0.10.0
bleach ==2.1.3
boltons ==18.0.0
boto ==2.46.1
bunch ==1.0.1
bx-python ==0.8.1
bz2file ==0.98
certifi ==2018.1.18
cffi ==1.11.5
chardet ==3.0.4
cheetah3 ==3.1.0
cliff ==2.11.0
cloudbridge ==0.3.3
cmd2 ==0.8.4
contextlib2 ==0.5.5
cryptography ==2.2.2
debtcollector ==1.19.0
decorator ==4.2.1
deprecation ==2.0.1
dictobj ==0.4
docopt ==0.6.2
docutils ==0.14
dogpile.cache ==0.6.5
enum34 ==1.1.6
fabric3 ==1.14.post1
funcsigs ==1.0.2
functools32 ==3.2.3.post2
future ==0.16.0
futures ==3.2.0
galaxy-sequence-utils ==1.1.2
globus-sdk ==1.3.0
h5py ==2.6.0
html5lib ==1.0.1
idna ==2.6
ipaddress ==1.0.19
iso8601 ==0.1.12
jmespath ==0.9.3
jsonpatch ==1.23
jsonpointer ==2.0
jsonschema ==2.6.0
keystoneauth1 ==3.4.0
kombu ==4.1.0
mako ==1.0.7
markupsafe ==1.0
mercurial ==3.7.3
monotonic ==1.4
msgpack ==0.5.6
munch ==2.3.1
netaddr ==0.7.19
netifaces ==0.10.6
nose ==1.3.7
numpy ==1.14.2
oauthlib ==2.0.7
openstacksdk ==0.12.0
os-client-config ==1.29.0
os-service-types ==1.2.0
osc-lib ==1.10.0
oslo.config ==6.0.2
oslo.i18n ==3.20.0
oslo.serialization ==2.25.0
oslo.utils ==3.36.0
packaging ==17.1
paramiko ==2.4.1
parsley ==1.3
paste ==2.0.3
pastedeploy ==1.5.2
pastescript ==2.0.2
pbr ==4.0.2
positional ==1.2.1
prettytable ==0.7.2
psutil ==5.4.3
pulsar-galaxy-lib ==0.8.3
py2-ipaddress ==3.4.1
pyasn1 ==0.4.2
pycparser ==2.18
pycrypto ==2.6.1
pycryptodomex ==3.6.0
pyjwkest ==1.4.0
pyjwt ==1.6.1
pykwalify ==1.6.1
pynacl ==1.2.1
pyparsing ==2.2.0
pyperclip ==1.6.0
pysam ==0.14.1
python-cinderclient ==2.0.1
python-dateutil ==2.7.2
python-genomespaceclient ==0.2
python-glanceclient ==2.6.0
python-keystoneclient ==3.10.0
python-lzo ==1.11
python-neutronclient ==6.1.0
python-novaclient ==7.0.0
python-openid ==2.2.5
python-swiftclient ==3.3.0
pytz ==2018.4
pyyaml ==3.12
repoze.lru ==0.7
requests ==2.18.4
requests-oauthlib ==0.8.0
requests-toolbelt ==0.8.0
requestsexceptions ==1.4.0
retrying ==1.3.3
rfc3986 ==1.1.0
routes ==2.4.1
simplejson ==3.13.2
six ==1.11.0
social-auth-core ==1.5.0
sqlalchemy ==1.2.6
sqlalchemy-migrate ==0.11.0
sqlalchemy-utils ==0.33.2
sqlparse ==0.2.4
stevedore ==1.28.0
subprocess32 ==3.5.0
svgwrite ==1.1.12
tempita ==0.5.2
tzlocal ==1.5.1
unicodecsv ==0.14.1
urllib3 ==1.22
uwsgi ==2.0.17
vine ==1.1.4
warlock ==1.2.0
wcwidth ==0.1.7
webencodings ==0.5.1
webob ==1.4.2
whoosh ==2.7.4
wrapt ==1.10.11

lib/galaxy/dependencies/pipfiles/develop/Pipfile pypi

NoseHTML *
Sphinx <1.7
lxml *
mock *
nodeenv *
pygithub3 *
recommonmark *
selenium *
sphinx_rtd_theme *
testfixtures *
twill ==0.9.1
watchdog *

lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock pypi

alabaster ==0.7.10
argh ==0.26.2
babel ==2.5.3
certifi ==2018.1.18
chardet ==3.0.4
commonmark ==0.5.4
docutils ==0.14
funcsigs ==1.0.2
idna ==2.6
imagesize ==1.0.0
jinja2 ==2.10
lxml ==4.2.1
markupsafe ==1.0
mock ==2.0.0
nodeenv ==1.3.0
nose ==1.3.7
nosehtml ==0.4.4
packaging ==17.1
pathtools ==0.1.2
pbr ==4.0.2
pygithub3 ==0.5.1
pygments ==2.2.0
pyparsing ==2.2.0
pytz ==2018.4
pyyaml ==3.12
recommonmark ==0.4.0
requests ==2.18.4
selenium ==3.11.0
six ==1.11.0
snowballstemmer ==1.2.1
sphinx ==1.6.7
sphinx-rtd-theme ==0.3.0
sphinxcontrib-websupport ==1.0.1
testfixtures ==6.0.0
twill ==0.9.1
typing ==3.6.4
urllib3 ==1.22
watchdog ==0.8.3

lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt pypi

alabaster ==0.7.10 development
argh ==0.26.2 development
babel ==2.5.3 development
certifi ==2018.1.18 development
chardet ==3.0.4 development
commonmark ==0.5.4 development
docutils ==0.14 development
funcsigs ==1.0.2 development
idna ==2.6 development
imagesize ==1.0.0 development
jinja2 ==2.10 development
lxml ==4.2.1 development
markupsafe ==1.0 development
mock ==2.0.0 development
nodeenv ==1.3.0 development
nose ==1.3.7 development
nosehtml ==0.4.4 development
packaging ==17.1 development
pathtools ==0.1.2 development
pbr ==4.0.2 development
pygithub3 ==0.5.1 development
pygments ==2.2.0 development
pyparsing ==2.2.0 development
pytz ==2018.4 development
pyyaml ==3.12 development
recommonmark ==0.4.0 development
requests ==2.18.4 development
selenium ==3.11.0 development
six ==1.11.0 development
snowballstemmer ==1.2.1 development
sphinx ==1.6.7 development
sphinx-rtd-theme ==0.3.0 development
sphinxcontrib-websupport ==1.0.1 development
testfixtures ==6.0.0 development
twill ==0.9.1 development
typing ==3.6.4 development
urllib3 ==1.22 development
watchdog ==0.8.3 development

lib/galaxy/dependencies/pipfiles/flake8/Pipfile pypi

flake8 *
flake8-import-order *

lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock pypi

configparser ==3.5.0
enum34 ==1.1.6
flake8 ==3.5.0
flake8-import-order ==0.17.1
mccabe ==0.6.1
pycodestyle ==2.3.1
pyflakes ==1.6.0

lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt pypi

configparser ==3.5.0
enum34 ==1.1.6
flake8 ==3.5.0
flake8-import-order ==0.17.1
mccabe ==0.6.1
pycodestyle ==2.3.1
pyflakes ==1.6.0

requirements.txt pypi

amqp ==2.2.2
appdirs ==1.4.3
asn1crypto ==0.24.0
babel ==2.5.3
bagit ==1.6.4
bcrypt ==3.1.4
bdbag ==1.2.4
beaker ==1.9.1
bioblend ==0.10.0
bleach ==2.1.3
boltons ==18.0.0
boto ==2.46.1
bunch ==1.0.1
bx-python ==0.8.1
bz2file ==0.98
certifi ==2018.1.18
cffi ==1.11.5
chardet ==3.0.4
cheetah3 ==3.1.0
cliff ==2.11.0
cloudbridge ==0.3.3
cmd2 ==0.8.4
contextlib2 ==0.5.5
cryptography ==2.2.2
debtcollector ==1.19.0
decorator ==4.2.1
deprecation ==2.0.1
dictobj ==0.4
docopt ==0.6.2
docutils ==0.14
dogpile.cache ==0.6.5
enum34 ==1.1.6
fabric3 ==1.14.post1
funcsigs ==1.0.2
functools32 ==3.2.3.post2
future ==0.16.0
futures ==3.2.0
galaxy-sequence-utils ==1.1.2
globus-sdk ==1.3.0
h5py ==2.6.0
html5lib ==1.0.1
idna ==2.6
ipaddress ==1.0.19
iso8601 ==0.1.12
jmespath ==0.9.3
jsonpatch ==1.23
jsonpointer ==2.0
jsonschema ==2.6.0
keystoneauth1 ==3.4.0
kombu ==4.1.0
mako ==1.0.7
markupsafe ==1.0
mercurial ==3.7.3
monotonic ==1.4
msgpack ==0.5.6
munch ==2.3.1
netaddr ==0.7.19
netifaces ==0.10.6
nose ==1.3.7
numpy ==1.14.2
oauthlib ==2.0.7
openstacksdk ==0.12.0
os-client-config ==1.29.0
os-service-types ==1.2.0
osc-lib ==1.10.0
oslo.config ==6.0.2
oslo.i18n ==3.20.0
oslo.serialization ==2.25.0
oslo.utils ==3.36.0
packaging ==17.1
paramiko ==2.4.1
parsley ==1.3
paste ==2.0.3
pastedeploy ==1.5.2
pastescript ==2.0.2
pbr ==4.0.2
positional ==1.2.1
prettytable ==0.7.2
psutil ==5.4.3
pulsar-galaxy-lib ==0.8.3
py2-ipaddress ==3.4.1
pyasn1 ==0.4.2
pycparser ==2.18
pycrypto ==2.6.1
pycryptodomex ==3.6.0
pyjwkest ==1.4.0
pyjwt ==1.6.1
pykwalify ==1.6.1
pynacl ==1.2.1
pyparsing ==2.2.0
pyperclip ==1.6.0
pysam ==0.14.1
python-cinderclient ==2.0.1
python-dateutil ==2.7.2
python-genomespaceclient ==0.2
python-glanceclient ==2.6.0
python-keystoneclient ==3.10.0
python-lzo ==1.11
python-neutronclient ==6.1.0
python-novaclient ==7.0.0
python-openid ==2.2.5
python-swiftclient ==3.3.0
pytz ==2018.4
pyyaml ==3.12
repoze.lru ==0.7
requests ==2.18.4
requests-oauthlib ==0.8.0
requests-toolbelt ==0.8.0
requestsexceptions ==1.4.0
retrying ==1.3.3
rfc3986 ==1.1.0
routes ==2.4.1
simplejson ==3.13.2
six ==1.11.0
social-auth-core ==1.5.0
sqlalchemy ==1.2.6
sqlalchemy-migrate ==0.11.0
sqlalchemy-utils ==0.33.2
sqlparse ==0.2.4
stevedore ==1.28.0
subprocess32 ==3.5.0
svgwrite ==1.1.12
tempita ==0.5.2
tzlocal ==1.5.1
unicodecsv ==0.14.1
urllib3 ==1.22
uwsgi ==2.0.17
vine ==1.1.4
warlock ==1.2.0
wcwidth ==0.1.7
webencodings ==0.5.1
webob ==1.4.2
whoosh ==2.7.4
wrapt ==1.10.11

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