MarkupSafe egg missing? e.args[1].key != e.args[0].key

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MarkupSafe egg missing? e.args[1].key != e.args[0].key

Peter Cock
Hello all,

There looks to be an egg problem with the latest galaxy-central,
here are excepts from a failed Galaxy install on my TravisCI test
setup,
https://travis-ci.org/peterjc/pico_galaxy/builds/41233860

Here's another project build with the same error:
https://travis-ci.org/peterjc/galaxy_blast/builds/41235899

$ ./run.sh --stop-daemon || true
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
...
Initializing static/welcome.html from welcome.html.sample
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg
Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg
Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 46, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
line 347, in resolve
    egg.resolve()
  File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
line 192, in resolve
    if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range
Fetch failed.
No PID file exists in paster.pid


$ python scripts/fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Traceback (most recent call last):
  File "scripts/fetch_eggs.py", line 46, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
line 347, in resolve
    egg.resolve()
  File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
line 192, in resolve
    if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range

The command "python scripts/fetch_eggs.py" failed and exited with 1

Looking at http://eggs.galaxyproject.org/MarkupSafe/ for
Python 2.7 and Linux x86_64 there is a ucs4 egg:

MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg        09-Jun-2011 03:09
            30724

So, why is this failing? Not I am not explicitly installing MakupSafe
(so I do not expect there to be a conflicting version installed).

Also it would seem there is a bug in the resolve method assuming that
e.arg will always have (at least) two entries?

Thanks,

Peter
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

saketkc
I have had the same issue. A little debugging here:
https://travis-ci.org/saketkc/galaxy_tools/builds/41209515#L84

I first thought that there was a conflict with system installed
paramiko, but it is not:
https://travis-ci.org/saketkc/galaxy_tools/builds/41210153#L60

A clean install of galaxy-central worked fine on Mac, I am yet to test
this on a local linux installation though.


On 17 November 2014 03:57, Peter Cock <[hidden email]> wrote:

> Hello all,
>
> There looks to be an egg problem with the latest galaxy-central,
> here are excepts from a failed Galaxy install on my TravisCI test
> setup,
> https://travis-ci.org/peterjc/pico_galaxy/builds/41233860
>
> Here's another project build with the same error:
> https://travis-ci.org/peterjc/galaxy_blast/builds/41235899
>
> $ ./run.sh --stop-daemon || true
> Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
> ...
> Initializing static/welcome.html from welcome.html.sample
> Some eggs are out of date, attempting to fetch...
> Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
> Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg
> Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg
> Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg
> Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg
> Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg
> Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
> Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
> Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg
> Traceback (most recent call last):
>   File "./scripts/fetch_eggs.py", line 46, in <module>
>     c.resolve() # Only fetch eggs required by the config
>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 347, in resolve
>     egg.resolve()
>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 192, in resolve
>     if e.args[1].key != e.args[0].key:
> IndexError: tuple index out of range
> Fetch failed.
> No PID file exists in paster.pid
>
>
> $ python scripts/fetch_eggs.py
> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> Traceback (most recent call last):
>   File "scripts/fetch_eggs.py", line 46, in <module>
>     c.resolve() # Only fetch eggs required by the config
>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 347, in resolve
>     egg.resolve()
>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 192, in resolve
>     if e.args[1].key != e.args[0].key:
> IndexError: tuple index out of range
>
> The command "python scripts/fetch_eggs.py" failed and exited with 1
>
> Looking at http://eggs.galaxyproject.org/MarkupSafe/ for
> Python 2.7 and Linux x86_64 there is a ucs4 egg:
>
> MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg        09-Jun-2011 03:09
>             30724
>
> So, why is this failing? Not I am not explicitly installing MakupSafe
> (so I do not expect there to be a conflicting version installed).
>
> Also it would seem there is a bug in the resolve method assuming that
> e.arg will always have (at least) two entries?
>
> Thanks,
>
> Peter
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

John Chilton-4
Ummm... I think it is that the VM started shipping with an
incompatible paramkio. Saket I think you were using -m like it were
-c?

> python -m "import string" # what you had
/usr/bin/python: No module named import string
> python -c "import string
> python -m "string"
>

Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv
and it works fine (reran today
https://travis-ci.org/jmchilton/bwa-mem/builds/37353814) - so I
suggest creating a virtualenv and testing Galaxy inside of that.

Hope this helps.

-John


On Mon, Nov 17, 2014 at 12:52 PM, Saket Choudhary <[hidden email]> wrote:

> I have had the same issue. A little debugging here:
> https://travis-ci.org/saketkc/galaxy_tools/builds/41209515#L84
>
> I first thought that there was a conflict with system installed
> paramiko, but it is not:
> https://travis-ci.org/saketkc/galaxy_tools/builds/41210153#L60
>
> A clean install of galaxy-central worked fine on Mac, I am yet to test
> this on a local linux installation though.
>
>
> On 17 November 2014 03:57, Peter Cock <[hidden email]> wrote:
>> Hello all,
>>
>> There looks to be an egg problem with the latest galaxy-central,
>> here are excepts from a failed Galaxy install on my TravisCI test
>> setup,
>> https://travis-ci.org/peterjc/pico_galaxy/builds/41233860
>>
>> Here's another project build with the same error:
>> https://travis-ci.org/peterjc/galaxy_blast/builds/41235899
>>
>> $ ./run.sh --stop-daemon || true
>> Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
>> ...
>> Initializing static/welcome.html from welcome.html.sample
>> Some eggs are out of date, attempting to fetch...
>> Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg
>> Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
>> Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg
>> Traceback (most recent call last):
>>   File "./scripts/fetch_eggs.py", line 46, in <module>
>>     c.resolve() # Only fetch eggs required by the config
>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 347, in resolve
>>     egg.resolve()
>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 192, in resolve
>>     if e.args[1].key != e.args[0].key:
>> IndexError: tuple index out of range
>> Fetch failed.
>> No PID file exists in paster.pid
>>
>>
>> $ python scripts/fetch_eggs.py
>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
>> Traceback (most recent call last):
>>   File "scripts/fetch_eggs.py", line 46, in <module>
>>     c.resolve() # Only fetch eggs required by the config
>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 347, in resolve
>>     egg.resolve()
>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>> line 192, in resolve
>>     if e.args[1].key != e.args[0].key:
>> IndexError: tuple index out of range
>>
>> The command "python scripts/fetch_eggs.py" failed and exited with 1
>>
>> Looking at http://eggs.galaxyproject.org/MarkupSafe/ for
>> Python 2.7 and Linux x86_64 there is a ucs4 egg:
>>
>> MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg        09-Jun-2011 03:09
>>             30724
>>
>> So, why is this failing? Not I am not explicitly installing MakupSafe
>> (so I do not expect there to be a conflicting version installed).
>>
>> Also it would seem there is a bug in the resolve method assuming that
>> e.arg will always have (at least) two entries?
>>
>> Thanks,
>>
>> Peter
>> ___________________________________________________________
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> 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:
>   http://lists.bx.psu.edu/
>
> 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
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

saketkc
On 17 November 2014 11:23, John Chilton <[hidden email]> wrote:

> Ummm... I think it is that the VM started shipping with an
> incompatible paramkio. Saket I think you were using -m like it were
> -c?
>
>> python -m "import string" # what you had
> /usr/bin/python: No module named import string
>> python -c "import string
>> python -m "string"
>>
>

Indeed. Thanks for pointing that out!
https://travis-ci.org/saketkc/galaxy_tools/builds/41283066#L60

Saket

> Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv
> and it works fine (reran today
> https://travis-ci.org/jmchilton/bwa-mem/builds/37353814) - so I
> suggest creating a virtualenv and testing Galaxy inside of that.
>
> Hope this helps.
>
> -John
>
>
> On Mon, Nov 17, 2014 at 12:52 PM, Saket Choudhary <[hidden email]> wrote:
>> I have had the same issue. A little debugging here:
>> https://travis-ci.org/saketkc/galaxy_tools/builds/41209515#L84
>>
>> I first thought that there was a conflict with system installed
>> paramiko, but it is not:
>> https://travis-ci.org/saketkc/galaxy_tools/builds/41210153#L60
>>
>> A clean install of galaxy-central worked fine on Mac, I am yet to test
>> this on a local linux installation though.
>>
>>
>> On 17 November 2014 03:57, Peter Cock <[hidden email]> wrote:
>>> Hello all,
>>>
>>> There looks to be an egg problem with the latest galaxy-central,
>>> here are excepts from a failed Galaxy install on my TravisCI test
>>> setup,
>>> https://travis-ci.org/peterjc/pico_galaxy/builds/41233860
>>>
>>> Here's another project build with the same error:
>>> https://travis-ci.org/peterjc/galaxy_blast/builds/41235899
>>>
>>> $ ./run.sh --stop-daemon || true
>>> Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
>>> ...
>>> Initializing static/welcome.html from welcome.html.sample
>>> Some eggs are out of date, attempting to fetch...
>>> Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg
>>> Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
>>> Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg
>>> Traceback (most recent call last):
>>>   File "./scripts/fetch_eggs.py", line 46, in <module>
>>>     c.resolve() # Only fetch eggs required by the config
>>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>>> line 347, in resolve
>>>     egg.resolve()
>>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>>> line 192, in resolve
>>>     if e.args[1].key != e.args[0].key:
>>> IndexError: tuple index out of range
>>> Fetch failed.
>>> No PID file exists in paster.pid
>>>
>>>
>>> $ python scripts/fetch_eggs.py
>>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
>>> Traceback (most recent call last):
>>>   File "scripts/fetch_eggs.py", line 46, in <module>
>>>     c.resolve() # Only fetch eggs required by the config
>>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>>> line 347, in resolve
>>>     egg.resolve()
>>>   File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
>>> line 192, in resolve
>>>     if e.args[1].key != e.args[0].key:
>>> IndexError: tuple index out of range
>>>
>>> The command "python scripts/fetch_eggs.py" failed and exited with 1
>>>
>>> Looking at http://eggs.galaxyproject.org/MarkupSafe/ for
>>> Python 2.7 and Linux x86_64 there is a ucs4 egg:
>>>
>>> MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg        09-Jun-2011 03:09
>>>             30724
>>>
>>> So, why is this failing? Not I am not explicitly installing MakupSafe
>>> (so I do not expect there to be a conflicting version installed).
>>>
>>> Also it would seem there is a bug in the resolve method assuming that
>>> e.arg will always have (at least) two entries?
>>>
>>> Thanks,
>>>
>>> Peter
>>> ___________________________________________________________
>>> 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:
>>>   http://lists.bx.psu.edu/
>>>
>>> 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:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

Peter Cock
In reply to this post by John Chilton-4
On Mon, Nov 17, 2014 at 7:23 PM, John Chilton <[hidden email]> wrote:
> Ummm... I think it is that the VM started shipping with an
> incompatible paramkio.
>
> [...]
>
> Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv
> and it works fine [...]

That's a useful workaround, but a virtualenv is not viable for existing
Galaxy installations - which may also come to have this problem if
their system copy of paramiko is updated?

I'm not familiar with paramiko or markupsafe, but if there is a conflict
it would be good to have a direct fix.

Peter
___________________________________________________________
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

John Chilton-4

Oops forgot to cc the list.

On Nov 18, 2014 7:26 AM, "John Chilton" <[hidden email]> wrote:

I will admit to not actually understanding Galaxy's dependency management but I think virtualenv is exactly the advice people who do understand it give http://dev.list.galaxyproject.org/Local-installation-problem-td4662627.html. It is a widely used tool precisely designed to solve such problems - I think it is the best way to go. I don't know why it would not be appropriate for existing installations - I think it is in fact somethimg of a "best practice" for existing installations.

Certainly that error message should be more helpful but I am not sure we should do anything to address this beyond that - do you have a particular idea in mind?

On Nov 18, 2014 5:49 AM, "Peter Cock" <[hidden email]> wrote:
On Mon, Nov 17, 2014 at 7:23 PM, John Chilton <[hidden email]> wrote:
> Ummm... I think it is that the VM started shipping with an
> incompatible paramkio.
>
> [...]
>
> Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv
> and it works fine [...]

That's a useful workaround, but a virtualenv is not viable for existing
Galaxy installations - which may also come to have this problem if
their system copy of paramiko is updated?

I'm not familiar with paramiko or markupsafe, but if there is a conflict
it would be good to have a direct fix.

Peter

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

Peter Cock
On Nov 18, 2014 7:26 AM, "John Chilton" <[hidden email]> wrote:
>
> I will admit to not actually understanding Galaxy's dependency management
> but I think virtualenv is exactly the advice people who do understand it
> give
> http://dev.list.galaxyproject.org/Local-installation-problem-td4662627.html.
> It is a widely used tool precisely designed to solve such problems - I think
> it is the best way to go. I don't know why it would not be appropriate for
> existing installations - I think it is in fact somethimg of a "best
> practice" for existing installations.

Our existing installation is not using a virtual env, and I fear switching to
that could be disruptive.

> Certainly that error message should be more helpful but I am not sure we
> should do anything to address this beyond that - do you have a particular
> idea in mind?

Not show the IndexError exception? :P

Here the user should be told something about a conflict between
MarkupSafe and paramiko (assuming this is the real problem).

Peter
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

Peter Cock
On Tue, Nov 18, 2014 at 1:24 PM, Peter Cock <[hidden email]> wrote:

> On Nov 18, 2014 7:26 AM, "John Chilton" <[hidden email]> wrote:
>>
>> I will admit to not actually understanding Galaxy's dependency management
>> but I think virtualenv is exactly the advice people who do understand it
>> give
>> http://dev.list.galaxyproject.org/Local-installation-problem-td4662627.html.
>> It is a widely used tool precisely designed to solve such problems - I think
>> it is the best way to go. I don't know why it would not be appropriate for
>> existing installations - I think it is in fact somethimg of a "best
>> practice" for existing installations.
>
> Our existing installation is not using a virtual env, and I fear switching to
> that could be disruptive.

Getting back to TravisCI, using a virtual env wasn't too painful:
https://github.com/peterjc/pico_galaxy/commit/26489a65a9cd60f9d055488d003346eab87941b0

I can now get back to tweaking the tests I was working on :)

Thanks,

Peter
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

Nate Coraor (nate@bx.psu.edu)
In reply to this post by Peter Cock
Peter,

Unless you've made modifications to Galaxy that depend on external
libraries, switching to a virtualenv for the server itself should be
pretty safe. Tools themselves can still run without using the/any
virtualenv, if desired.

--nate

On Tue, Nov 18, 2014 at 8:24 AM, Peter Cock <[hidden email]> wrote:

> On Nov 18, 2014 7:26 AM, "John Chilton" <[hidden email]> wrote:
>>
>> I will admit to not actually understanding Galaxy's dependency management
>> but I think virtualenv is exactly the advice people who do understand it
>> give
>> http://dev.list.galaxyproject.org/Local-installation-problem-td4662627.html.
>> It is a widely used tool precisely designed to solve such problems - I think
>> it is the best way to go. I don't know why it would not be appropriate for
>> existing installations - I think it is in fact somethimg of a "best
>> practice" for existing installations.
>
> Our existing installation is not using a virtual env, and I fear switching to
> that could be disruptive.
>
>> Certainly that error message should be more helpful but I am not sure we
>> should do anything to address this beyond that - do you have a particular
>> idea in mind?
>
> Not show the IndexError exception? :P
>
> Here the user should be told something about a conflict between
> MarkupSafe and paramiko (assuming this is the real problem).
>
> Peter
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Re: MarkupSafe egg missing? e.args[1].key != e.args[0].key

Peter Cock
On Tue, Nov 18, 2014 at 5:51 PM, Nate Coraor <[hidden email]> wrote:
> Peter,
>
> Unless you've made modifications to Galaxy that depend on external
> libraries, switching to a virtualenv for the server itself should be
> pretty safe. Tools themselves can still run without using the/any
> virtualenv, if desired.
>
> --nate

OK - that sounds more straightforward than I had feared - but I
will cross that bridge as needed ;)

Thanks,

Peter
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