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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">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 "XXXXXXXX/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.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
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 peter.briggs@manchester.ac.uk 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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">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 "XXXXXXXX/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.briggs@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/
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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-v1xxxxxxxx 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: 7.0-0 conda-forge setuptools: 38.5.1-py27_0 conda-forge sqlite: 3.20.1-2 conda-forge tk: 8.6.7-0 conda-forge wheel: 0.30.0-py27_2 conda-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 p.j.a.cock@googlemail.com 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 peter.briggs@manchester.ac.uk 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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">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 "XXXXXXXX/galaxy-tools/tools/pal_finder/pal_filter.py", line129
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.briggs@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/
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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.vandenbeek@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-v1xxxxxxxx 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: 7.0-0 conda-forge setuptools: 38.5.1-py27_0 conda-forge sqlite: 3.20.1-2 conda-forge tk: 8.6.7-0 conda-forge wheel: 0.30.0-py27_2 conda-forge zlib: 1.2.11-0 conda-forgeSo 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 p.j.a.cock@googlemail.com 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 peter.briggs@manchester.ac.uk 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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">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 "XXXXXXXX/galaxy-tools/tools/pal_finder/pal_filter.py", line129 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.briggs@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/
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.cock@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.vandenbeek@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-v1xxxxxxxx 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: 7.0-0 conda-forge setuptools: 38.5.1-py27_0 conda-forge sqlite: 3.20.1-2 conda-forge tk: 8.6.7-0 conda-forge wheel: 0.30.0-py27_2 conda-forge zlib: 1.2.11-0 conda-forgeSo 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 p.j.a.cock@googlemail.com 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 peter.briggs@manchester.ac.uk 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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">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 "XXXXXXXX/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.briggs@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/
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&sort_order=d...
Peter
On Mon, Mar 5, 2018 at 5:00 PM, Marius van den Beek m.vandenbeek@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.cock@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.vandenbeek@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-v1xxxxxxxx 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: 7.0-0 conda-forge setuptools: 38.5.1-py27_0 conda-forge sqlite: 3.20.1-2 conda-forge tk: 8.6.7-0 conda-forge wheel: 0.30.0-py27_2 conda-forge zlib: 1.2.11-0 conda-forgeSo 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 p.j.a.cock@googlemail.com 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 peter.briggs@manchester.ac.uk 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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package"version="1.65">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 "XXXXXXXX/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.briggs@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/
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.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
________________________________________ From: Peter Cock [p.j.a.cock@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&sort_order=d...
Peter
On Mon, Mar 5, 2018 at 5:00 PM, Marius van den Beek m.vandenbeek@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.cock@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.vandenbeek@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-v1xxxxxxxx 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: 7.0-0 conda-forge setuptools: 38.5.1-py27_0 conda-forge sqlite: 3.20.1-2 conda-forge tk: 8.6.7-0 conda-forge wheel: 0.30.0-py27_2 conda-forge zlib: 1.2.11-0 conda-forgeSo 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 p.j.a.cock@googlemail.com 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 peter.briggs@manchester.ac.uk 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:
<requirement type="package" version="2.7">python</requirement> <requirement type="package"version="1.65">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 "XXXXXXXX/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.briggs@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/
galaxy-dev@lists.galaxyproject.org
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Marius van den Beek -
Peter Briggs -
Peter Cock