Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-06 Thread Peter Briggs 
Hello Marius and Peter

Thanks for all the info & suggestions, that was really helpful and I can see 
what's happening now (and why it's not working in my specific case).

If you're interested in the details:

-- If the tool requires python==2.7 and biopython=1.65 only, then as Marius 
says the dependencies are resolved and Galaxy creates a "mulled" environment 
with the correct package versions installed.

-- In my case however I have some additional requirements defined, which are 
not yet in bioconda or the other channels (at this stage they've just been 
built locally, while I try to get everything updated). In this case conda fails 
to resolve some of the dependencies when trying to create the mulled 
environment, and bails out - instead it creates individual environments (e.g. 
__python@2.7, __biopython@1.65 etc) just for those packages it can find. But 
this fallback "standalone" biopython environment doesn't have the python==2.7 
requirement transferred in, hence it defaults to python3.

I guess I didn't have this issue previously when migrating other tools (even 
when there were local dependencies) as there was no python dependency in those 
cases.

So it looks like I need to sort out the missing dependencies first, then come 
back to testing the tool.

Thanks again both for all your help,

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482



From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Monday, March 05, 2018 5:04 PM
To: Marius van den Beek
Cc: Peter Briggs; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies 
for tool

Oh yeah - thanks, I can see them in the default channel which does have
far older versions of Biopython packaged - currently 1.65 is on page 5:

https://anaconda.org/anaconda/biopython/files?sort=basename_order=desc=5

Peter


On Mon, Mar 5, 2018 at 5:00 PM, Marius van den Beek
<m.vandenb...@gmail.com> wrote:
> It's coming from the defaults channel, I didn't check if this is actually
> working,
> it may very well not be compatible with the remaining packages form
> conda-forge.
> AFAIK you can't specify packages to install via the regular conda commands
> (though you can use pip in a conda environemnt to do this manually).
>
> Hope that helps,
> Marius
>
> On 5 March 2018 at 17:51, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>>
>> I stand corrected. Looking closer, there are conda packages
>> for both Python 2 and 3, e.g.
>>
>> https://anaconda.org/conda-forge/biopython/files
>>
>> However, in this case you're asking for an older Biopython
>> which has to date not been packaged in conda-forge or
>> bioconda, so I presume in Marius example it comes from
>> PyPI via pip?
>>
>>
>> Peter
>>
>> On Mon, Mar 5, 2018 at 4:46 PM, Marius van den Beek
>> <m.vandenb...@gmail.com> wrote:
>> > This should actually work properly if you install the dependencies via
>> > the Manage dependencies page in the admin menu or if you install the
>> > tool
>> > via the tool shed.
>> > This translates more or less to the following conda command:
>> > ```
>> > $ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc -c
>> > bioconda -c conda-forge -c defaults
>> > Fetching package metadata ...
>> > Solving package specifications: .
>> >
>> > Package plan for installation in environment
>> > /Users/mvandenb/miniconda3/envs/test_resolution:
>> >
>> > The following NEW packages will be INSTALLED:
>> >
>> > biopython:   1.65-np19py27_0
>> > ca-certificates: 2018.1.18-0  conda-forge
>> > certifi: 2018.1.18-py27_0 conda-forge
>> > intel-openmp:2018.0.0-h8158457_8
>> > libgfortran: 3.0.1-h93005f0_2
>> > mkl: 2018.0.1-hfbd8650_4
>> > ncurses: 5.9-10   conda-forge
>> > numpy:   1.9.3-py27hb3dd696_3
>> > openssl: 1.0.2n-0 conda-forge
>> > pip: 9.0.1-py27_1 conda-forge
>> > python:  2.7.14-4 conda-forge
>> > readline:7.0-0conda-forge
>> > setuptools:  38.5.1-py27_0conda-forge
>> > sqlite:  3.20.1-2 conda-forge
>> > tk:  8.6.7-0  conda-forge
>> > wheel:   0.30.0-py27_2conda-forge
>> > zlib:1.2.11-0

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Cock 
Oh yeah - thanks, I can see them in the default channel which does have
far older versions of Biopython packaged - currently 1.65 is on page 5:

https://anaconda.org/anaconda/biopython/files?sort=basename_order=desc=5

Peter


On Mon, Mar 5, 2018 at 5:00 PM, Marius van den Beek
 wrote:
> It's coming from the defaults channel, I didn't check if this is actually
> working,
> it may very well not be compatible with the remaining packages form
> conda-forge.
> AFAIK you can't specify packages to install via the regular conda commands
> (though you can use pip in a conda environemnt to do this manually).
>
> Hope that helps,
> Marius
>
> On 5 March 2018 at 17:51, Peter Cock  wrote:
>>
>> I stand corrected. Looking closer, there are conda packages
>> for both Python 2 and 3, e.g.
>>
>> https://anaconda.org/conda-forge/biopython/files
>>
>> However, in this case you're asking for an older Biopython
>> which has to date not been packaged in conda-forge or
>> bioconda, so I presume in Marius example it comes from
>> PyPI via pip?
>>
>>
>> Peter
>>
>> On Mon, Mar 5, 2018 at 4:46 PM, Marius van den Beek
>>  wrote:
>> > This should actually work properly if you install the dependencies via
>> > the Manage dependencies page in the admin menu or if you install the
>> > tool
>> > via the tool shed.
>> > This translates more or less to the following conda command:
>> > ```
>> > $ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc -c
>> > bioconda -c conda-forge -c defaults
>> > Fetching package metadata ...
>> > Solving package specifications: .
>> >
>> > Package plan for installation in environment
>> > /Users/mvandenb/miniconda3/envs/test_resolution:
>> >
>> > The following NEW packages will be INSTALLED:
>> >
>> > biopython:   1.65-np19py27_0
>> > ca-certificates: 2018.1.18-0  conda-forge
>> > certifi: 2018.1.18-py27_0 conda-forge
>> > intel-openmp:2018.0.0-h8158457_8
>> > libgfortran: 3.0.1-h93005f0_2
>> > mkl: 2018.0.1-hfbd8650_4
>> > ncurses: 5.9-10   conda-forge
>> > numpy:   1.9.3-py27hb3dd696_3
>> > openssl: 1.0.2n-0 conda-forge
>> > pip: 9.0.1-py27_1 conda-forge
>> > python:  2.7.14-4 conda-forge
>> > readline:7.0-0conda-forge
>> > setuptools:  38.5.1-py27_0conda-forge
>> > sqlite:  3.20.1-2 conda-forge
>> > tk:  8.6.7-0  conda-forge
>> > wheel:   0.30.0-py27_2conda-forge
>> > zlib:1.2.11-0 conda-forge
>> > ```
>> >
>> > So given a recent conda (latest version should work) and the correct
>> > channel
>> > order
>> > it should work.
>> >
>> > Best,
>> > Marius
>> >
>> > On 5 March 2018 at 17:39, Peter Cock  wrote:
>> >>
>> >> Tricky, as I understand it the conda python packages are specific to
>> >> the conda version of Python - in this case Python 3 not 2.
>> >>
>> >> It might actually be simpler to fix pal_finder/pal_filter.py to cope
>> >> with Python 3 - is the code online somewhere, I could probably cast an
>> >> eye over it.
>> >>
>> >> Peter
>> >>
>> >> On Mon, Mar 5, 2018 at 4:28 PM, Peter Briggs
>> >>  wrote:
>> >> > Hello
>> >> >
>> >> > I'm in the process of updating our local Galaxy tools to use conda
>> >> > dependency resolution, and I've hit a snag with a tool that requires
>> >> > Python
>> >> > 2.7 along with the Python 2.7-compatible version of Biopython 1.65.
>> >> >
>> >> > I'd assumed that if I explicitly used the following in the
>> >> > "requirements" section of the tool XML:
>> >> >
>> >> > python
>> >> > > >> > version="1.65">biopython
>> >> >
>> >> > that the biopython install would respect the specified Python
>> >> > version,
>> >> > and that the command execution environment would be based on Python
>> >> > 2.7.
>> >> >
>> >> > But in practice it appears I'm getting Python3 as I'm seeing errors:
>> >> >
>> >> >   File "/galaxy-tools/tools/pal_finder/pal_filter.py",
>> >> > line
>> >> > 129
>> >> > print "\n~~"
>> >> >^
>> >> > SyntaxError: Missing parentheses in call to 'print'
>> >> >
>> >> > This is happening both when running the tool tests via the planemo
>> >> > tests, and also when I install the tool from a local toolshed
>> >> > instance.
>> >> >
>> >> > Can anyone advise how to coerce the Python dependencies to be
>> >> > 2.7-compatible?
>> >> >
>> >> > Thanks in advance for any help,
>> >> >
>> >> > Best wishes
>> >> >
>> >> > Peter
>> >> >
>> >> > --
>> >> > Peter Briggs peter.bri...@manchester.ac.uk
>> >> > Bioinformatics Core Facility University of Manchester
>> >> > B.1083 Michael Smith Bldg Tel: (0161) 2751482
>> >> >
>> >> >

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Marius van den Beek 
It's coming from the defaults channel, I didn't check if this is actually
working,
it may very well not be compatible with the remaining packages form
conda-forge.
AFAIK you can't specify packages to install via the regular conda commands
(though you can use pip in a conda environemnt to do this manually).

Hope that helps,
Marius

On 5 March 2018 at 17:51, Peter Cock  wrote:

> I stand corrected. Looking closer, there are conda packages
> for both Python 2 and 3, e.g.
>
> https://anaconda.org/conda-forge/biopython/files
>
> However, in this case you're asking for an older Biopython
> which has to date not been packaged in conda-forge or
> bioconda, so I presume in Marius example it comes from
> PyPI via pip?
>
>
> Peter
>
> On Mon, Mar 5, 2018 at 4:46 PM, Marius van den Beek
>  wrote:
> > This should actually work properly if you install the dependencies via
> > the Manage dependencies page in the admin menu or if you install the tool
> > via the tool shed.
> > This translates more or less to the following conda command:
> > ```
> > $ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc -c
> > bioconda -c conda-forge -c defaults
> > Fetching package metadata ...
> > Solving package specifications: .
> >
> > Package plan for installation in environment
> > /Users/mvandenb/miniconda3/envs/test_resolution:
> >
> > The following NEW packages will be INSTALLED:
> >
> > biopython:   1.65-np19py27_0
> > ca-certificates: 2018.1.18-0  conda-forge
> > certifi: 2018.1.18-py27_0 conda-forge
> > intel-openmp:2018.0.0-h8158457_8
> > libgfortran: 3.0.1-h93005f0_2
> > mkl: 2018.0.1-hfbd8650_4
> > ncurses: 5.9-10   conda-forge
> > numpy:   1.9.3-py27hb3dd696_3
> > openssl: 1.0.2n-0 conda-forge
> > pip: 9.0.1-py27_1 conda-forge
> > python:  2.7.14-4 conda-forge
> > readline:7.0-0conda-forge
> > setuptools:  38.5.1-py27_0conda-forge
> > sqlite:  3.20.1-2 conda-forge
> > tk:  8.6.7-0  conda-forge
> > wheel:   0.30.0-py27_2conda-forge
> > zlib:1.2.11-0 conda-forge
> > ```
> >
> > So given a recent conda (latest version should work) and the correct
> channel
> > order
> > it should work.
> >
> > Best,
> > Marius
> >
> > On 5 March 2018 at 17:39, Peter Cock  wrote:
> >>
> >> Tricky, as I understand it the conda python packages are specific to
> >> the conda version of Python - in this case Python 3 not 2.
> >>
> >> It might actually be simpler to fix pal_finder/pal_filter.py to cope
> >> with Python 3 - is the code online somewhere, I could probably cast an
> >> eye over it.
> >>
> >> Peter
> >>
> >> On Mon, Mar 5, 2018 at 4:28 PM, Peter Briggs
> >>  wrote:
> >> > Hello
> >> >
> >> > I'm in the process of updating our local Galaxy tools to use conda
> >> > dependency resolution, and I've hit a snag with a tool that requires
> Python
> >> > 2.7 along with the Python 2.7-compatible version of Biopython 1.65.
> >> >
> >> > I'd assumed that if I explicitly used the following in the
> >> > "requirements" section of the tool XML:
> >> >
> >> > python
> >> > biopython requirement>
> >> >
> >> > that the biopython install would respect the specified Python version,
> >> > and that the command execution environment would be based on Python
> 2.7.
> >> >
> >> > But in practice it appears I'm getting Python3 as I'm seeing errors:
> >> >
> >> >   File "/galaxy-tools/tools/pal_finder/pal_filter.py",
> line
> >> > 129
> >> > print "\n~~"
> >> >^
> >> > SyntaxError: Missing parentheses in call to 'print'
> >> >
> >> > This is happening both when running the tool tests via the planemo
> >> > tests, and also when I install the tool from a local toolshed
> instance.
> >> >
> >> > Can anyone advise how to coerce the Python dependencies to be
> >> > 2.7-compatible?
> >> >
> >> > Thanks in advance for any help,
> >> >
> >> > Best wishes
> >> >
> >> > Peter
> >> >
> >> > --
> >> > Peter Briggs peter.bri...@manchester.ac.uk
> >> > Bioinformatics Core Facility University of Manchester
> >> > B.1083 Michael Smith Bldg Tel: (0161) 2751482
> >> >
> >> > ___
> >> > 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/
> >> ___
> >> Please keep all

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Cock 
I stand corrected. Looking closer, there are conda packages
for both Python 2 and 3, e.g.

https://anaconda.org/conda-forge/biopython/files

However, in this case you're asking for an older Biopython
which has to date not been packaged in conda-forge or
bioconda, so I presume in Marius example it comes from
PyPI via pip?


Peter

On Mon, Mar 5, 2018 at 4:46 PM, Marius van den Beek
 wrote:
> This should actually work properly if you install the dependencies via
> the Manage dependencies page in the admin menu or if you install the tool
> via the tool shed.
> This translates more or less to the following conda command:
> ```
> $ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc -c
> bioconda -c conda-forge -c defaults
> Fetching package metadata ...
> Solving package specifications: .
>
> Package plan for installation in environment
> /Users/mvandenb/miniconda3/envs/test_resolution:
>
> The following NEW packages will be INSTALLED:
>
> biopython:   1.65-np19py27_0
> ca-certificates: 2018.1.18-0  conda-forge
> certifi: 2018.1.18-py27_0 conda-forge
> intel-openmp:2018.0.0-h8158457_8
> libgfortran: 3.0.1-h93005f0_2
> mkl: 2018.0.1-hfbd8650_4
> ncurses: 5.9-10   conda-forge
> numpy:   1.9.3-py27hb3dd696_3
> openssl: 1.0.2n-0 conda-forge
> pip: 9.0.1-py27_1 conda-forge
> python:  2.7.14-4 conda-forge
> readline:7.0-0conda-forge
> setuptools:  38.5.1-py27_0conda-forge
> sqlite:  3.20.1-2 conda-forge
> tk:  8.6.7-0  conda-forge
> wheel:   0.30.0-py27_2conda-forge
> zlib:1.2.11-0 conda-forge
> ```
>
> So given a recent conda (latest version should work) and the correct channel
> order
> it should work.
>
> Best,
> Marius
>
> On 5 March 2018 at 17:39, Peter Cock  wrote:
>>
>> Tricky, as I understand it the conda python packages are specific to
>> the conda version of Python - in this case Python 3 not 2.
>>
>> It might actually be simpler to fix pal_finder/pal_filter.py to cope
>> with Python 3 - is the code online somewhere, I could probably cast an
>> eye over it.
>>
>> Peter
>>
>> On Mon, Mar 5, 2018 at 4:28 PM, Peter Briggs
>>  wrote:
>> > Hello
>> >
>> > I'm in the process of updating our local Galaxy tools to use conda
>> > dependency resolution, and I've hit a snag with a tool that requires Python
>> > 2.7 along with the Python 2.7-compatible version of Biopython 1.65.
>> >
>> > I'd assumed that if I explicitly used the following in the
>> > "requirements" section of the tool XML:
>> >
>> > python
>> > biopython
>> >
>> > that the biopython install would respect the specified Python version,
>> > and that the command execution environment would be based on Python 2.7.
>> >
>> > But in practice it appears I'm getting Python3 as I'm seeing errors:
>> >
>> >   File "/galaxy-tools/tools/pal_finder/pal_filter.py", line
>> > 129
>> > print "\n~~"
>> >^
>> > SyntaxError: Missing parentheses in call to 'print'
>> >
>> > This is happening both when running the tool tests via the planemo
>> > tests, and also when I install the tool from a local toolshed instance.
>> >
>> > Can anyone advise how to coerce the Python dependencies to be
>> > 2.7-compatible?
>> >
>> > Thanks in advance for any help,
>> >
>> > Best wishes
>> >
>> > Peter
>> >
>> > --
>> > Peter Briggs peter.bri...@manchester.ac.uk
>> > Bioinformatics Core Facility University of Manchester
>> > B.1083 Michael Smith Bldg Tel: (0161) 2751482
>> >
>> > ___
>> > 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/
>> ___
>> 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/
>
>
___
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/

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Marius van den Beek 
This should actually work properly if you install the dependencies via
the Manage dependencies page in the admin menu or if you install the tool
via the tool shed.
This translates more or less to the following conda command:
```
$ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc -c
bioconda -c conda-forge -c defaults
Fetching package metadata ...
Solving package specifications: .

Package plan for installation in environment
/Users/mvandenb/miniconda3/envs/test_resolution:

The following NEW packages will be INSTALLED:

biopython:   1.65-np19py27_0
ca-certificates: 2018.1.18-0  conda-forge
certifi: 2018.1.18-py27_0 conda-forge
intel-openmp:2018.0.0-h8158457_8
libgfortran: 3.0.1-h93005f0_2
mkl: 2018.0.1-hfbd8650_4
ncurses: 5.9-10   conda-forge
numpy:   1.9.3-py27hb3dd696_3
openssl: 1.0.2n-0 conda-forge
pip: 9.0.1-py27_1 conda-forge
python:  2.7.14-4 conda-forge
readline:7.0-0conda-forge
setuptools:  38.5.1-py27_0conda-forge
sqlite:  3.20.1-2 conda-forge
tk:  8.6.7-0  conda-forge
wheel:   0.30.0-py27_2conda-forge
zlib:1.2.11-0 conda-forge
```

So given a recent conda (latest version should work) and the correct
channel order
it should work.

Best,
Marius

On 5 March 2018 at 17:39, Peter Cock  wrote:

> Tricky, as I understand it the conda python packages are specific to
> the conda version of Python - in this case Python 3 not 2.
>
> It might actually be simpler to fix pal_finder/pal_filter.py to cope
> with Python 3 - is the code online somewhere, I could probably cast an
> eye over it.
>
> Peter
>
> On Mon, Mar 5, 2018 at 4:28 PM, Peter Briggs
>  wrote:
> > Hello
> >
> > I'm in the process of updating our local Galaxy tools to use conda
> dependency resolution, and I've hit a snag with a tool that requires Python
> 2.7 along with the Python 2.7-compatible version of Biopython 1.65.
> >
> > I'd assumed that if I explicitly used the following in the
> "requirements" section of the tool XML:
> >
> > python
> > biopython
> >
> > that the biopython install would respect the specified Python version,
> and that the command execution environment would be based on Python 2.7.
> >
> > But in practice it appears I'm getting Python3 as I'm seeing errors:
> >
> >   File "/galaxy-tools/tools/pal_finder/pal_filter.py", line
> 129
> > print "\n~~"
> >^
> > SyntaxError: Missing parentheses in call to 'print'
> >
> > This is happening both when running the tool tests via the planemo
> tests, and also when I install the tool from a local toolshed instance.
> >
> > Can anyone advise how to coerce the Python dependencies to be
> 2.7-compatible?
> >
> > Thanks in advance for any help,
> >
> > Best wishes
> >
> > Peter
> >
> > --
> > Peter Briggs peter.bri...@manchester.ac.uk
> > Bioinformatics Core Facility University of Manchester
> > B.1083 Michael Smith Bldg Tel: (0161) 2751482
> >
> > ___
> > 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/
> ___
> 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/
>
___
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/

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Cock 
Tricky, as I understand it the conda python packages are specific to
the conda version of Python - in this case Python 3 not 2.

It might actually be simpler to fix pal_finder/pal_filter.py to cope
with Python 3 - is the code online somewhere, I could probably cast an
eye over it.

Peter

On Mon, Mar 5, 2018 at 4:28 PM, Peter Briggs
 wrote:
> Hello
>
> I'm in the process of updating our local Galaxy tools to use conda dependency 
> resolution, and I've hit a snag with a tool that requires Python 2.7 along 
> with the Python 2.7-compatible version of Biopython 1.65.
>
> I'd assumed that if I explicitly used the following in the "requirements" 
> section of the tool XML:
>
> python
> biopython
>
> that the biopython install would respect the specified Python version, and 
> that the command execution environment would be based on Python 2.7.
>
> But in practice it appears I'm getting Python3 as I'm seeing errors:
>
>   File "/galaxy-tools/tools/pal_finder/pal_filter.py", line 129
> print "\n~~"
>^
> SyntaxError: Missing parentheses in call to 'print'
>
> This is happening both when running the tool tests via the planemo tests, and 
> also when I install the tool from a local toolshed instance.
>
> Can anyone advise how to coerce the Python dependencies to be 2.7-compatible?
>
> Thanks in advance for any help,
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
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[galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Briggs 
Hello

I'm in the process of updating our local Galaxy tools to use conda dependency 
resolution, and I've hit a snag with a tool that requires Python 2.7 along with 
the Python 2.7-compatible version of Biopython 1.65.

I'd assumed that if I explicitly used the following in the "requirements" 
section of the tool XML:

python
biopython

that the biopython install would respect the specified Python version, and that 
the command execution environment would be based on Python 2.7.

But in practice it appears I'm getting Python3 as I'm seeing errors:

  File "/galaxy-tools/tools/pal_finder/pal_filter.py", line 129
print "\n~~"
   ^
SyntaxError: Missing parentheses in call to 'print'

This is happening both when running the tool tests via the planemo tests, and 
also when I install the tool from a local toolshed instance.

Can anyone advise how to coerce the Python dependencies to be 2.7-compatible?

Thanks in advance for any help,

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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