conda management of tools dependent on python3
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
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/
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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 __<package>@<package_version> <package>==<package_version python=3.5 -c bioconda (following the example at https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-d...), 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 <package> 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/
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 __<package>@<package_version> <package>==<package_version python=3.5 -c bioconda
(following the example at https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-d...), 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 <package> 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/
I'm not quite sure if I understand you correctly, but let's see. The original tool wrapper stated <requirement type="package" version="3.4">python3</requirement> 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: <requirement type="package" version="3.4">python</requirement> 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 __<package>@<package_version> <package>==<package_version python=3.5 -c bioconda
(following the example at https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-d...), 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 <package> 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/
Dear All, I try to filter options for a param linked to a datatable. I want to keep only options with the same dbkey as my input file. But i cannot make it work. <param name="input" type="data" format="bam" label="Bam file"/> <param name="dbindel" type="select" force_select="true" label="indel database"> <options from_data_table="dbindel" /> <filter type="data_meta" ref="input" key="dbkey" /> <filter type="remove_value" key="dbkey"/> </param> ##dbindels #<unique_build_id> <dbkey> <display_name> <file_path> hg38 hg38 Human /data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf mm10_1 mm10 Mouse [All] /data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz mm10_2 mm10 Mouse [129P2_OlaHsd] /data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz Thank you for help, Vincent
Hi Vincent, have you defined the dbindel table in config/tool_data_table_conf.xml ? Cheers, Nicola On 04/11/16 08:09, Vincent Cahais wrote:
Dear All,
I try to filter options for a param linked to a datatable. I want to keep only options with the same dbkey as my input file. But i cannot make it work.
<param name="input" type="data" format="bam" label="Bam file"/> <param name="dbindel" type="select" force_select="true" label="indel database"> <options from_data_table="dbindel" /> <filter type="data_meta" ref="input" key="dbkey" /> <filter type="remove_value" key="dbkey"/> </param>
##dbindels #<unique_build_id> <dbkey> <display_name> <file_path> hg38 hg38 Human /data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf mm10_1 mm10 Mouse [All] /data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz mm10_2 mm10 Mouse [129P2_OlaHsd] /data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz
Thank you for help,
Vincent ___________________________________________________________ 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/
Sure, my combo-box is correctly filled with all options, but unfiltered. <table comment_char="#" name="dbindel"> <columns>value, dbkey, name, path</columns> <file path="****" /> </table> </tables> Le 04/11/2016 à 13:42, Nicola Soranzo a écrit :
Hi Vincent, have you defined the dbindel table in config/tool_data_table_conf.xml ?
Cheers, Nicola
On 04/11/16 08:09, Vincent Cahais wrote:
Dear All,
I try to filter options for a param linked to a datatable. I want to keep only options with the same dbkey as my input file. But i cannot make it work.
<param name="input" type="data" format="bam" label="Bam file"/> <param name="dbindel" type="select" force_select="true" label="indel database"> <options from_data_table="dbindel" /> <filter type="data_meta" ref="input" key="dbkey" /> <filter type="remove_value" key="dbkey"/> </param>
##dbindels #<unique_build_id> <dbkey> <display_name> <file_path> hg38 hg38 Human /data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf mm10_1 mm10 Mouse [All] /data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz mm10_2 mm10 Mouse [129P2_OlaHsd] /data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz
Thank you for help,
Vincent ___________________________________________________________ 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/
I found the solution : <param name="input" type="data" format="bam" label="Bam file"/> <param name="dbindel" type="select" force_select="true" label="indel database"> <options from_data_table="dbindel"> <filter type="data_meta" ref="input" key="dbkey" column="1"/> </options> </param> Le 04/11/2016 à 13:50, Vincent Cahais a écrit : Sure, my combo-box is correctly filled with all options, but unfiltered. <table comment_char="#" name="dbindel"> <columns>value, dbkey, name, path</columns> <file path="****" /> </table> </tables> Le 04/11/2016 à 13:42, Nicola Soranzo a écrit : Hi Vincent, have you defined the dbindel table in config/tool_data_table_conf.xml ? Cheers, Nicola On 04/11/16 08:09, Vincent Cahais wrote: Dear All, I try to filter options for a param linked to a datatable. I want to keep only options with the same dbkey as my input file. But i cannot make it work. <param name="input" type="data" format="bam" label="Bam file"/> <param name="dbindel" type="select" force_select="true" label="indel database"> <options from_data_table="dbindel" /> <filter type="data_meta" ref="input" key="dbkey" /> <filter type="remove_value" key="dbkey"/> </param> ##dbindels #<unique_build_id> <dbkey> <display_name> <file_path> hg38 hg38 Human /data/genome/hg38/dbindel/Mills_and_1000G_gold_standard.indels.hg38.vcf mm10_1 mm10 Mouse [All] /data/genomes/mm10/dbindel/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz mm10_2 mm10 Mouse [129P2_OlaHsd] /data/genome/mm10/dbindel/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz Thank you for help, Vincent ___________________________________________________________ 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/ -- Vincent Cahais, Sr Resrch Asst Data Mg/Anlys Programming Tech, Mecanisms of Carcinogenesis Section International Agency for Research on Cancer World Health Organization 150 cours Albert Thomas 69372 Lyon CEDEX 08, France Off. +33 472 738 487 Mob. E-mail:cahaisv@iarc.fr<mailto:cahaisv@iarc.fr> [cid:part2.865F1581.1CD08F04@iarc.fr]<https://www.iarc.fr/index.php>
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
<requirement type="package" version="3.4">python3</requirement>
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:
<requirement type="package" version="3.4">python</requirement>
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 __<package>@<package_version> <package>==<package_version python=3.5 -c bioconda
(following the example at https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-d...),
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 <package> 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/
participants (4)
-
Björn Grüning -
Nicola Soranzo -
Vincent Cahais -
Wolfgang Maier