Hi Stephen and Nate,
it seems that the problem with the WebError egg
is now hitting also BioBlend TravisCI


for Python 2.6 and 2.7, scripts/common_startup.sh fails

"WebError 0.8a couldn't be downloaded automatically. You can
building it by hand with:
python scripts/scramble.py -c
config/galaxy.ini.sample -e WebError
Fetch failed."

Please note that
this has been working fine for 6 months (last TravisCI build 19 days
ago) and is still working on my laptops.


Il 08.02.2015 04:35
Stephen Rosen ha scritto: 

> It took me a couple of extra days to get
the time to test this, sorry about the delay.
> The initial run:
WebError 0.8a couldn't be downloaded automatically. You can try
building it by hand with:
> python scripts/scramble.py -e WebError
Fetch failed.
> When I patch a traceback.print_exc() into
fetch_eggs.py , this is what I see:
> Some eggs are out of date,
attempting to fetch...
> Warning: sqlalchemy (a dependent egg of
sqlalchemy-migrate) cannot be fetched
> Traceback (most recent call
> File "./scripts/fetch_eggs.py", line 36, in 
> c.resolve() #
Only fetch eggs required by the config
> File
"/opt/galaxy/lib/galaxy/eggs/__init__.py", line 349, in resolve
> raise
EggNotFetchable( missing )
> EggNotFetchable: 
> WebError 0.8a couldn't
be downloaded automatically. You can try
> building it by hand with:
python scripts/scramble.py -e WebError
> Fetch failed.
> If I look
into lib/galaxy/eggs , that line is here:
> In the current galaxy source, that is here:
> As a bit of an aside, I really do have to install this other
package in the same python that galaxy uses, since it's one of the major
parts of our fork -- not part of our custom tools. 
> I wouldn't
consider this a normal use case of course, but I'll bet that many people
will install galaxy with system python, which can lead to similar
> Please let me know if I can provide any other useful
information on what I'm seeing.
> Again, thanks for looking into this
with me, 
> -Stephen 
> On Thu, Feb 5, 2015 at 8:19 AM, Nate Coraor
>> Hi Stephen, 
>> On Wed, Feb 4, 2015 at 8:30 PM, Stephen
Rosen wrote:
>>> Hi Nate,
>>> Thanks so much for helping me out
with this.
>>> It seems that I've miscommunicated what I'm doing a
little bit. I'm installing a package from that git repo using pip
separately from running the galaxy setup script. That is, I want to
install a python package and I want to setup galaxy as two separate (and
ideally independent) steps in my script. 
>>> I have no desire to do
anything particularly esoteric or clever with Galaxy's eggs or to
install them myself. Somehow, doing a pip install of my desired package
is breaking the later run of fetch_eggs.py
>>> If I understand you
correctly, fetch_eggs.py can hit conflicts with site-packages, but is
misreporting them as EggNotFetchable. 
>>> I am aware that we're using a
fork of the Galaxy source ( https://bitbucket.org/galaxycloud/galaxy/src
[1] ), so it may be that we have an outdated of fetch_eggs.py which
carries a bug that has since been patched. 
>>> Sorry for not mentioning
it earlier -- it slipped my mind that we're probably trailing behind the
modern Galaxy default head. 
>>> If I put in the extra legwork now
to wrap Galaxy in a virtualenv, this issue will presumably disappear,
but that assumes that I don't want to add any packages to the python
used for the uwsgi process.
>> You can add additional packages to
this virtualenv, although there could be problems if you install
different versions of the same packages that Galaxy has as dependencies.
For what it's worth, you should not need to install additional packages
in Galaxy's virtualenv, and tools can be configured to use a different
python or virtualenv than the one in which Galaxy is started. 
I'll have to ask folks on the Globus Genomics team whether or not that
is needed -- I certainly hope not, since it means that there is some
packaging conflict we need to resolve. 
>>> The only reason I haven't
done so already is time constraint -- I've been trying to get this
install scripting done as quickly as possible without compromising
anything truly needful. 
>>> All the same, I'll take some time
tomorrow to provision a fresh server and generate the stacktrace for
>>> I'll also take some time to test with the latest Galaxy
source, to see if I get different behavior. 
>>> In the best case, this
bug no longer exists for the modern source, but in the worst case it
bears the attention.
>> Thanks for the help with debugging. 
I don't have any sense of the reliability of fetch_eggs.py and company
-- my experience has been of a particular bug that presented on my first
contact with thes
>>> finally settled on a package manager, even if
we can't seem to agree on a package format or tooling surrounding it.

>>> That's just an opinion though -- I have no blog post from Guido to
back it up. 
>>> I hope we'll see the necessary improvements within the
next year, but I think anything we do now will essentially reinvent the
wheel (no pun intended) with regards to what will (hopefully) be
officially implemented to fix the problem. 
>>> --nate
>> I was not
aware of the UCS2 vs. UCS4 issue -- thanks very much for the citations,
very helpful in understanding the problem space. 
>> Thanks,
>> -Stephen

>> On Wed, Feb 4, 2015 at 5:41 PM, Nate Coraor c solid;
padding-left: 1ex;"> 
>>> Hi Stephen, 
>>> I'll try to reply as in-depth
as I can. 
>>> On Wed, Feb 4, 2015 at 1:41 PM, Stephen Rosen
>>>> 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
>>>> 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 forward. 
>>> 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 [2] , 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
>>> 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
>>>> br
/>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
>>>> In case someone else wants to test to replicate, this
is the command being used: 
>>>> pip install --egg
>>>> 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.
>>> ltr"> 
>>> 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 us
>>>> of
the Galaxy application. 
>>>> 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
>>> n 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 [9]
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 h
>>>> ll 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
>>> nstall .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 packages. 
>>> [1]
>>> [2] http://lucumr.pocoo.org/2014/1/27/python-on-wheels/ [11]

>>> 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
[4] , 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
>>>> 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
>>> n'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 la
>>>> ut 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 t
>>> d 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 t

>>>> Barring even that improvement, the Wiki page at
https://wiki.galaxyproject.org/Admin/Config/Eggs [5] 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
>>> 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 [12] 
>>> - Galaxy
should probably default to using pip when it's available, since its
failure modes 
>>>> many thanks for your time and attention, 
>>>> 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/ [6]
>>>> To search Galaxy mailing
lists use the unified search at:
http://galaxyproject.org/search/mailinglists/ [7]

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