Re: [galaxy-dev] conda management of tools dependent on python3
Hi Wolfgang, I guess that the conda recipe should be updated to also specify - python >=3 in the requirements. Cheers, Nicola On 03/11/16 21:04, Wolfgang Maier wrote: I'm not quite sure if I understand you correctly, but let's see. The original tool wrapper stated python3 as a dependency. This did not work with at runtime installation at all because conda cannot resolve python3 and the requirement got ignored by Galaxy. I changed the requirement tag now to: python and now Galaxy happily installs a __python@3.4 environment, but then it tries to set up a *new* environment for my package, which is still based on python2.7 and fails as before. On the bioconda side, all the recipe does is to declare that it shouldn't be built under python2 using skip: True # [py2k] in the build section of the recipe. On 03.11.2016 21:36, Björn Grüning wrote: Hi, can you check the package? The package should have a dependency on python3, if not the package seems to be broken :( Ciao, Bjoern Am 03.11.2016 um 21:32 schrieb Wolfgang Maier: Hi Björn, Hmm, I guess I should have phrased my question more clearly. What I'm trying to do is to get Galaxy to satisfy a missing tool dependency at *tool runtime* using a bioconda package that is only available for Python3. I am able to satisfy the dependency *manually* by running: conda create --name __@ ==https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), but when I let *Galaxy autoinstall* the package it will use python2.7 for the environment, then fail with: Error: Unsatisfiable package specifications. and a hint that conflicts with python 2.7. So my question is: is there any way to inform Galaxy that the dependency requires a conda environment based on python3? Best, Wolfgang On 28.10.2016 19:14, Björn Grüning wrote: Hi Wolfgang, can you describe step by step what you are trying to do? A conda package ships it's own python version, you can see this in the build-string py35_0 for example. So conda can handle all python version independent of the python version of miniconda. Cheers, Bjoern Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a tool dependency that has a conda package built for only python3 I'm getting an error because of a conflict between that package and python2 (not surprisingly), but AFAIU conda environments are bound to one particular version of python (or is that incorrect?). Thanks for any help with this and best wishes, Wolfgang ___ 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/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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] conda management of tools dependent on python3
I'm not quite sure if I understand you correctly, but let's see. The original tool wrapper stated python3 as a dependency. This did not work with at runtime installation at all because conda cannot resolve python3 and the requirement got ignored by Galaxy. I changed the requirement tag now to: python and now Galaxy happily installs a __python@3.4 environment, but then it tries to set up a *new* environment for my package, which is still based on python2.7 and fails as before. On the bioconda side, all the recipe does is to declare that it shouldn't be built under python2 using skip: True # [py2k] in the build section of the recipe. On 03.11.2016 21:36, Björn Grüning wrote: Hi, can you check the package? The package should have a dependency on python3, if not the package seems to be broken :( Ciao, Bjoern Am 03.11.2016 um 21:32 schrieb Wolfgang Maier: Hi Björn, Hmm, I guess I should have phrased my question more clearly. What I'm trying to do is to get Galaxy to satisfy a missing tool dependency at *tool runtime* using a bioconda package that is only available for Python3. I am able to satisfy the dependency *manually* by running: conda create --name __@ ==https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), but when I let *Galaxy autoinstall* the package it will use python2.7 for the environment, then fail with: Error: Unsatisfiable package specifications. and a hint that conflicts with python 2.7. So my question is: is there any way to inform Galaxy that the dependency requires a conda environment based on python3? Best, Wolfgang On 28.10.2016 19:14, Björn Grüning wrote: Hi Wolfgang, can you describe step by step what you are trying to do? A conda package ships it's own python version, you can see this in the build-string py35_0 for example. So conda can handle all python version independent of the python version of miniconda. Cheers, Bjoern Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a tool dependency that has a conda package built for only python3 I'm getting an error because of a conflict between that package and python2 (not surprisingly), but AFAIU conda environments are bound to one particular version of python (or is that incorrect?). Thanks for any help with this and best wishes, Wolfgang ___ 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/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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] conda management of tools dependent on python3
Hi, can you check the package? The package should have a dependency on python3, if not the package seems to be broken :( Ciao, Bjoern Am 03.11.2016 um 21:32 schrieb Wolfgang Maier: > Hi Björn, > > Hmm, I guess I should have phrased my question more clearly. What I'm > trying to do is to get Galaxy to satisfy a missing tool dependency at > *tool runtime* using a bioconda package that is only available for > Python3. I am able to satisfy the dependency *manually* by running: > > conda create --name __@ > == > (following the example at > https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), > but when I let *Galaxy autoinstall* the package it will use python2.7 > for the environment, then fail with: > > Error: Unsatisfiable package specifications. > > and a hint that conflicts with python 2.7. So my question is: > is there any way to inform Galaxy that the dependency requires a conda > environment based on python3? > > Best, > Wolfgang > > > On 28.10.2016 19:14, Björn Grüning wrote: >> Hi Wolfgang, >> >> can you describe step by step what you are trying to do? >> >> A conda package ships it's own python version, you can see this in the >> build-string py35_0 for example. So conda can handle all python version >> independent of the python version of miniconda. >> >> Cheers, >> Bjoern >> >>> Dear all, >>> >>> I'm still pretty new to conda tool dependencies management and there is >>> one thing I cannot find documented anywhere: >>> How can I let conda manage tool dependencies that involve python3? >>> If I let Galaxy install conda for me, it creates an environment with >>> python2, then if there is a tool dependency that has a conda package >>> built for only python3 I'm getting an error because of a conflict >>> between that package and python2 (not surprisingly), but AFAIU conda >>> environments are bound to one particular version of python (or is that >>> incorrect?). >>> >>> Thanks for any help with this and best wishes, >>> Wolfgang >>> ___ >>> 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/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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] conda management of tools dependent on python3
Hi Björn, Hmm, I guess I should have phrased my question more clearly. What I'm trying to do is to get Galaxy to satisfy a missing tool dependency at *tool runtime* using a bioconda package that is only available for Python3. I am able to satisfy the dependency *manually* by running: conda create --name __@ == (following the example at https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), but when I let *Galaxy autoinstall* the package it will use python2.7 for the environment, then fail with: Error: Unsatisfiable package specifications. and a hint that conflicts with python 2.7. So my question is: is there any way to inform Galaxy that the dependency requires a conda environment based on python3? Best, Wolfgang On 28.10.2016 19:14, Björn Grüning wrote: Hi Wolfgang, can you describe step by step what you are trying to do? A conda package ships it's own python version, you can see this in the build-string py35_0 for example. So conda can handle all python version independent of the python version of miniconda. Cheers, Bjoern Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a tool dependency that has a conda package built for only python3 I'm getting an error because of a conflict between that package and python2 (not surprisingly), but AFAIU conda environments are bound to one particular version of python (or is that incorrect?). Thanks for any help with this and best wishes, Wolfgang ___ 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/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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] conda management of tools dependent on python3
Hi Wolfgang, can you describe step by step what you are trying to do? A conda package ships it's own python version, you can see this in the build-string py35_0 for example. So conda can handle all python version independent of the python version of miniconda. Cheers, Bjoern > Dear all, > > I'm still pretty new to conda tool dependencies management and there is > one thing I cannot find documented anywhere: > How can I let conda manage tool dependencies that involve python3? > If I let Galaxy install conda for me, it creates an environment with > python2, then if there is a tool dependency that has a conda package > built for only python3 I'm getting an error because of a conflict > between that package and python2 (not surprisingly), but AFAIU conda > environments are bound to one particular version of python (or is that > incorrect?). > > Thanks for any help with this and best wishes, > Wolfgang > ___ > 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/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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
