Nate Coraor
04af1ae1c6
Always use the python hashlib for verifying the virtualenv download in
...
common_startup.sh rather than attempting to use sha256sum. Older
versions of coreutils (such as in RHEL 6) did not include the --strict
argument to sha256sum.
2016-02-03 13:16:27 -05:00
Dannon Baker
6635e91170
Bump gx pip version to fix OSX platform issues.
2016-02-02 10:45:14 -05:00
Nate Coraor
60062b020d
pip 1.6 -> 6.0, thanks @nsoranzo
2016-01-28 12:46:14 -05:00
Nate Coraor
46471d61e4
pip < 1.6 cannot parse requirement specifiers to the install command
...
that contain a `+` in the version. For these older versions, directly
install the wheel or install from the sdist. Technically 1.4 and later
can install wheels, but in testing, only 1.5+ was able to install them
properly with their scripts.
The new heredoc execute and redirect syntax is Bourne-compatible.
pip --pre is no longer necessary since the Galaxy pip version is no
longer a development version of pip.
2016-01-28 10:45:54 -05:00
Nate Coraor
390c1fc275
Always install a specific version of Galaxy pip in common_startup.sh.
2016-01-27 09:57:41 -05:00
Nate Coraor
8ceb4d8ee4
Force --skip-venv if we can detect that Python is Conda Python.
2016-01-21 11:49:51 -05:00
John Chilton
8fd83df665
Allow override of location of virtual env Galaxy manages.
2016-01-13 13:55:36 +00:00
John Chilton
9dc9ddf8cd
Add --replace-pip option to common_startup.sh.
...
Needed to restore correct functionality to planemo.
2016-01-13 13:55:35 +00:00
Nate Coraor
4eefd885ec
Improve startup options related to wheel/dependency/virtualenv
...
management. Drop hard requirement on lzo (doubt anyone other than
usegalaxy.org is using it, but it will be added as a extras option for
bxlab/bx-python for anyone who is).
Fixes #1150
2015-12-22 14:03:50 -05:00
Nate Coraor
43e38414e6
--pre does not exist on pip < 1.4, but on pip < 1.4, the default
...
behavior was the same as using --pre on pip >= 1.4. Therefore, detect
the version of pip and add --pre if necessary.
Fixes #1134
2015-12-18 12:27:12 -05:00
Nate Coraor
1a3a594d4e
Allow CentOS to install RHEL wheels.
2015-10-26 15:47:51 -04:00
Nate Coraor
d90ba82e92
Add a --dev-wheels arg to common_startup.sh (called by run_tests.sh by
...
default) that will install things in dev-requirements.txt.
2015-10-26 14:07:00 -04:00
Nate Coraor
88683c3c40
Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is
...
provided.
2015-10-22 18:42:06 -04:00
Nate Coraor
4a5f5f44dc
Install our modified pip as a wheel from wheels.galaxyproject.org rather
...
than an editable directly from github.
Also, use `set -e` in scripts/common_startup.sh to fail if anything
fails, rather than chaining a bunch of things with `&&` but not properly
handling failure cases.
2015-10-22 15:02:14 -04:00
Nate Coraor
d92787557a
Move vvers and vurl vars to a more relevant scope.
2015-10-15 11:00:50 -04:00
Nate Coraor
433b79de2b
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
2015-10-13 16:54:18 -04:00
Nate Coraor
744835bbfe
Allow the use of common_startup.sh's --skip-eggs from run_tests.sh, and
...
have tox pass this flag (so that dependencies are installed in the tox
envs)
2015-10-13 12:47:01 -04:00
Nate Coraor
665c4c299d
Handle the case where there are no conditional (heh) requirements
2015-10-01 15:38:58 -04:00
Nate Coraor
a44b2c2170
Rename galaxy.wheels to the more generalized galaxy.dependencies (since
...
technically we don't care whether they are wheels), handle optional deps
more correctly. Add error handling to common_startup.sh.
2015-09-22 12:54:03 -04:00
Nate Coraor
40bde6e102
Install required dependencies from requirements.txt rather than
...
convoluted galaxy.wheels method. Not sure why I was doing that.
Hackathons are dangerous places.
2015-09-21 13:21:13 -04:00
Lance Parsons
5810a853b0
Move manual_builds.txt to manual_builds.txt.sample to allow for customization
2015-08-18 14:00:30 -04:00
Nate Coraor
5501917346
Install modified pip in develop/edit mode so it won't be reinstalled
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every time (courtesy @jxtx).
2015-07-05 10:50:54 -04:00
Nate Coraor
a24134c447
Install modified pip for fetching Linux wheels, fetch wheels from
...
wheels.galaxyproject.org
2015-07-05 05:24:15 -04:00
Nate Coraor
633061f3e0
WIP: Stop using eggs, start using prebuilt wheels.
2015-07-04 15:18:50 -04:00
Nate Coraor
92f6ace47f
Ensure the correct default Galaxy config file is found in common_startup.sh, it
...
makes a difference for egg fetching since some eggs are conditional based on
config.
2015-02-12 11:47:58 -05:00
Nate Coraor
267e4d9b88
Don't create galaxy.ini, just use the sample if galaxy.ini does not exist. Also fix startup when galaxy.ini.sample. Fixes the universe_wsgi.ini skipping problem Dannon found.
2014-09-15 22:12:18 -04:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Nate Coraor
4227d0eabb
Remove additional pieces from old genome index system.
2014-07-27 02:48:40 -04:00
Dave Bouvier
4e63bc8731
Fetch eggs after initializing sample files, per John Chilton's comment.
2014-06-13 17:32:51 -04:00
Dave Bouvier
8b45411adf
Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh.
2014-06-13 16:39:59 -04:00
Nate Coraor