Lets wait until this potential problem materializes before we address
it with a sourcing attribute. Dependencies should be appending or
prepending to common paths or otherwise they should be setting up
environment variables that are just required for that individual
package or tool, so there should
> The potential problem I see here is that environment variables are not
> name spaced in any way, so if all env.sh files are sourced no matter
> what, there is the potential for a certain environment variable to get
> set to a certain dependency version, and then later during the
> installation
Please see my inline comments. Thanks!
Greg Von Kuster
On Nov 7, 2013, at 1:33 PM, John Chilton wrote:
> On Thu, Nov 7, 2013 at 1:46 AM, Björn Grüning
> wrote:
>> Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
>>
>> My two cents below.
>>
>> On Wed, Nov 6, 2013 at 4:20 P
On Thu, Nov 7, 2013 at 1:46 AM, Björn Grüning
wrote:
> Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
>
> My two cents below.
>
> On Wed, Nov 6, 2013 at 4:20 PM, Björn Grüning
> wrote:
>> Hi Dave,
>>
>>> We're thinking that the following approach makes the most sense:
>>>
>>> O
Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
> My two cents below.
>
> On Wed, Nov 6, 2013 at 4:20 PM, Björn Grüning
> wrote:
> > Hi Dave,
> >
> >> We're thinking that the following approach makes the most sense:
> >>
> >> OR >> type="setup_r_environment"> OR OR
> >>
> >>
My two cents below.
On Wed, Nov 6, 2013 at 4:20 PM, Björn Grüning
wrote:
> Hi Dave,
>
>> We're thinking that the following approach makes the most sense:
>>
>> OR > type="setup_r_environment"> OR OR
>>
>> > name="package_perl_5_18" owner="iuc"
>> toolshed="http://testtoolshed.g2.bx.psu.ed
Hi Dave,
> We're thinking that the following approach makes the most sense:
>
> OR type="setup_r_environment"> OR OR
>
> name="package_perl_5_18" owner="iuc"
> toolshed="http://testtoolshed.g2.bx.psu.edu";>
>
>
> name="package_expat_2_1" owner="iuc"
> toolshed="
Björn,
We're thinking that the following approach makes the most sense:
OR type="setup_r_environment"> OR OR
name="package_perl_5_18" owner="iuc"
toolshed="http://testtoolshed.g2.bx.psu.edu";>
name="package_expat_2_1" owner="iuc"
toolshed="http://testtoolshed.g2.bx.p
Hi John,
> Perl complicates things, TPP complicates things greatly.
So true, so true ...
> Bjoern, can I ask you if this hypothetical exhibits the same problem
> and can be used to reason about these things more easily and drive a
> test implementation.
Yes to both questions :)
> So right now,
Perl complicates things, TPP complicates things greatly.
Bjoern, can I ask you if this hypothetical exhibits the same problem
and can be used to reason about these things more easily and drive a
test implementation.
So right now, Galaxy has setup_virtualenv which will build and install
Python pac
Thanks Björn,
We'll have to digest this a bit and we'll get back to you.
Greg Von Kuster
On Nov 5, 2013, at 4:35 PM, Björn Grüning
wrote:
> Hi Greg,
>
>> Hello Bjoern,
>>
>>
>> On Nov 5, 2013, at 12:13 PM, Bjoern Gruening
>> wrote:
>>
>> > Hi Greg,
>> >
>> > I'm right now in implementi
Hi Greg,
> Hello Bjoern,
>
>
> On Nov 5, 2013, at 12:13 PM, Bjoern Gruening
> wrote:
>
> > Hi Greg,
> >
> > I'm right now in implementing a setup_perl_environment and stumbled about a
> > tricky problem (that is not only related to perl but also for ruby, python
> > and R).
> >
> > The P
Hello Bjoern,
On Nov 5, 2013, at 12:13 PM, Bjoern Gruening wrote:
> Hi Greg,
>
> I'm right now in implementing a setup_perl_environment and stumbled about a
> tricky problem (that is not only related to perl but also for ruby, python
> and R).
>
> The Problem:
> Lets assume a perl package (
Hi Greg,
I'm right now in implementing a setup_perl_environment and stumbled
about a tricky problem (that is not only related to perl but also for
ruby, python and R).
The Problem:
Lets assume a perl package (A) requires a xml parser written in C/C++
(Z).
(Z) is a dependency that I can import but
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