Hi Stephen,

I'll try to reply as in-depth as I can.

On Wed, Feb 4, 2015 at 1:41 PM, Stephen Rosen <siro...@uchicago.edu> wrote:

> Hi Galaxy Dev,
> I've been looking at the setup scripts for Galaxy to try to understand a
> problem I recently had provisioning a Galaxy server.
> I will readily admit that I have not read all of the relevant code
> top-to-bottom, but I have at least skimmed all of it and read much of it.
> Sorry if these questions are answered somewhere in Trello, the Wiki, or
> somewhere else, but I was not able to find answers in any public locations.
> As a small bit of probably irrelevant context:
> I'm working with the Globus Genomics group on the DevOps side of things.
> We're using Chef.
> I've only just started working with the group in the past couple of weeks
> (so my expertise with Galaxy itself is limited to nonexistent).
> First, to describe the problem:
> We want to provision a server running Galaxy without explicitly wrapping
> it in a virtualenv.
> Unless I missed something, that means that it's using system python.
> When we use pip to install a package from a git repository before running
> the setup scripts, fetch_eggs fails saying it failed to fetch WebError 0.8a
> If we install the same package from git with `pip install --egg ...` we
> get a hunky-dory system where everything seems to work.

A virtualenv is itself just a wrapper around whichever python binary was
used to create it. I'd still suggest using a virtualenv created with the
system python unless you have a really strong reason not to. In fact, I'm
working on Galaxy process management and a command line tool for that
management that will automatically create and use a virtualenv going

I'm a bit confused at what's happening here - you mention installing a
package from a git repository with pip, but then refer to Galaxy's
fetch_eggs(.py) script, which doesn't use pip or git.

> As far as I can tell, there is no reason that this should be the case.
> Sure, putting the git source directly into site-packages might cause
> issues upon installation, but EggNotFetchable exceptions should only be
> thrown if the egg actually can't be pulled down from eggs.g2.bx.psu.edu ,
> right?

EggNotFetchable can be thrown if you happen to be using a platform for
which we do not provide eggs, although those are fairly uncommon. Right now
we should cover x86/x86_64 Linux and any flavor of Intel OS X after 10.5.

> I don't feel comfortable trying to make further progress on my
> provisioning scripts without knowing why this is happening.
> I'd hate to be bitten by this later on in the process.
> Yes, the package in question may have poor behavior (likely it does), but
> that doesn't change the fact that the error is totally misleading.
> Furthermore, it doesn't appear that this poor behavior impedes me from
> doing a pip install of the WebError package or any other packages from PyPI.
> In case someone else wants to test to replicate, this is the command being
> used:
>   pip install --egg git+
> https://github.com/globusonline/python-nexus-client@599f04edef6b72569b7a5b272b0b847dcda3ea99#egg=nexus-client
> problems occur if you omit `--egg`.

None of this process is using Galaxy's egg handling, so I am not sure where
the EggNotFetchable is coming from. What command are you running to get an
EggNotFetchable error.

> Second, a question about the rationale for Galaxy's egg handling:
> Why is all of this wrapped up in these scripts in the first place?
> I understand that pip might not be present on every platform, and I don't
> mean to question a decision to support systems without it.
> However, as detailed below, Galaxy does not support any platforms which
> are incapable of running pip.

This isn't the case - Galaxy does not use pip to install the framework
dependencies at all. Some tool dependencies installed from the Tool Shed do
use pip, but that's entirely separate from the dependencies of the Galaxy

The `scripts/scramble.py` script can be used to automatically build eggs on
platforms which we do not prebuild eggs for. If this is necessary,
`scripts/fetch_eggs.py` should tell you.

> Furthermore, pip is being pushed by the Python maintainers over
> easy_install, so it's not like there isn't a clear choice in terms of which
> one to support.
> Perhaps most importantly, there don't appear to be any clear-cut options
> to do the following, which I would consider a more ordinary workflow:
> - Run a galaxy script (like check_eggs) to generate a list of packages
> from eggs.g2.bx.psu.edu for platform (redirect output to requirements.txt
> or similar)
> - `pip install -r requirements.txt`

This is exactly what `scripts/check_eggs.py` and `scripts/fetch_eggs.py` do.

There are 3 reasons for the way we handle eggs in Galaxy:

1. Galaxy has a huge (and ever-growing) list of dependent python modules
with C extensions. If we did not prebuild and distribute eggs for these,
the initial setup to get Galaxy running would be long and problematic. Some
people who download Galaxy to develop tools may not even have compilers
installed, let alone the multitude of -dev or -devel packages that aren't
part of a default Debian or RHEL installation that would be required to
build all of these packages from source. One of the things that I feel
makes Galaxy so accessible is that you can start using it immediately after
you clone the source. So that ability to clone and start and have it work
as reliably (and quickly) as possible is a high priority.

2. Galaxy started using eggs in 2005 or 2006. At this time, everything used
distutils. pkg_resources came around, which soon brought setuptools and
easy_install. After this came distutils2, pip and finally, these days,
wheels. Our need for binary dependency packaging predated almost all of
these (in fact, most packages in these days didn't even install .egg-info,
which was the only reliable way to know what version of a module you were
using) and as each new iteration of packaging/management came along it was
never clear that any of them had "won" (and in fact, most of them lost). On
top of this, the Python packaging folks have known for years that Python's
platform detection for binary compatibility is broken[1]. While I was
assured it'd be fixed soon, even with a complete reimplementation of Python
packaging (wheels), they still haven't even made an effort to fix this
problem[2]. In fact, binary wheels for Linux are explicitly not allowed on
PyPI because of this.

3. We tightly control the versions of all of our dependencies, which is not
always possible with pip if you aren't also controlling the source of your

[1] https://mail.python.org/pipermail/distutils-sig/2010-January/015345.html
[2] http://lucumr.pocoo.org/2014/1/27/python-on-wheels/

The above could be part of a galaxy provisioning script, rather than
> exposed to the administrator.
> That also makes it significantly easier to control and manage the
> virtualenv in which we run Galaxy, since we don't have to worry about
> egg-related logic that we don't control and we know that the virtualenv's
> bin dir will be earlier in the PATH than the system pip's dir.
> Yes, I said above that our setup is presently using system python --
> switching to a virtualenv is one of the many items on my to-do list.
> In fact, I would expect that the default, desired setup for Galaxy would
> be to put it in a virtualenv, rather than using system python, and to use
> pip, rather than fetch_eggs.py and company.

A virtualenv is indeed the strongly preferred setup as I mentioned above.
However, Galaxy does not install its eggs to the virtualenv. The virtualenv
is there to avoid conflicts with things in the default python's
site-packages/dist-packages. Galaxy's eggs are installed to (by default)
the `eggs/` directory in the Galaxy source.

However, the problem, as I now see it, is that you are trying to install
all of Galaxy's dependencies, even at their correct versions, using pip,
rather than letting Galaxy handle its eggs as it does. This is not going to
work, Galaxy is going to insist on using its eggs.

> When I look at the logic being used here, especially at
> https://bitbucket.org/galaxy/galaxy-central/src/f0ae870b22e9/lib/galaxy/eggs/?at=default
> , it looks like a solution built exclusively for platforms on which pip is
> not installed.
> According to the wiki, Galaxy support only goes back as far as 2.6, and
> get-pip.py supports 2.6, so there is no way of building a Galaxy server on
> a platform that can't also have pip installed.
> Adding pip to the requirements for Galaxy would not be particularly
> onerous, and may simplify things significantly (no need to bundle
> get-pip.py or similar).

As mentioned above, we don't use or depend on pip, so it's not required.
That said, a lot of our egg fetching logic could likely be replaced with
pip (this code predates pip by a few years). And the eggs could probably be
replaced with prebuilt wheels. However, even if we did use pip/wheels, we'd
need to install them from our own repository, and it'd still require
modifications for binary platform incompatibilities. The egg handling code
we have now works pretty reliably, so I am not sure there is a whole lot to
be gained by changing it until Python finally figures out how to handle
binary compatibility properly.

> As a last note about the misleading error from the fetch_eggs script,
> telling me that WebError is "NotFetchable".
> I probably wouldn't have much of a complaint about this if the error had
> been more on target and I hadn't felt the need to do things like patch
> lib/galaxy/eggs to print a stacktrace.
> For example, if the script detected that there was a source installed
> package which was getting underfoot, it should have alerted me or even
> suggested installing my various packages in egg format.

This is a bug - it is supposed to explain that there is a version conflict.
If you have a stack trace, please send it along.

> That kind of error detection is hard to maintain and hard to keep accurate
> since the Galaxy team's priority is to build Galaxy, not a package manager.
> This, I suppose, circles back to an earlier question: why isn't Galaxy
> using a python package manager to... manage its packages?
> At the very least something along the lines of `./scripts/common_setup.sh
> --use-pip` should be added.
> It doesn't seem like it would be that hard to implement -- but I feel like
> my lack of knowledge of Galaxy disqualifies me from building the changeset
> reliably.
> Of course, if no one objects, I will readily do so anyway (when I have the
> time) as a proof of concept.

There are modifications to a few of the dependencies, such as psycopg2.
When psycopg2 is scrambled, the scrambling process fetches and compiles a
bit of PostgreSQL's libpq and then statically links to it to provide a
standalone egg that does not depend on the user having installed libpq on
their system. So a pip-based system that allowed building from source would
need to account for this.


> Barring even that improvement, the Wiki page at
> https://wiki.galaxyproject.org/Admin/Config/Eggs should definitely be
> updated to include some note on why Galaxy has this complex logic for
> fetching eggs instead of using pip.
> A quick tl;dr and summary:
> - I don't have extensive experience with Galaxy, so I may not know what
> I'm talking about.
> - fetch_eggs.py can be made to raise EggNotFetchable by doing a pip
> install from a VCS without using `--egg`. This is a bug in fetch_eggs.py
> - All supported platforms for Galaxy support pip
> - Galaxy should have an option to use pip to download its packages over
> https from eggs.g2.bx.psu.edu
> - Galaxy should probably default to using pip when it's available, since
> its failure modes are significantly better than a home-brewed package
> manager -- this also leads to good behavior in virtualenvs.
> Best regards, and many thanks for your time and attention,
> -Stephen
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to