devteam dropped support for installing tool dependencies from toolshed?
Dear developers It looks like some updates to 'devteam'-maintained toolshed tools have dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so their dependencies cannot be automatically installed from the toolshed. Is this correct? I assume that it's part of the move to enforcing conda dependency resolution. Best wishes Peter -- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hi Peter, Am 15.12.2016 um 11:28 schrieb Peter Briggs:
Dear developers
It looks like some updates to 'devteam'-maintained toolshed tools have dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so their dependencies cannot be automatically installed from the toolshed. Is this correct? I assume that it's part of the move to enforcing conda dependency resolution.
Yes. We really hope we are ready to go for conda, John and Marius have improved the conda support dramatically in the last months. Thanks, Bjoern
Best wishes
Peter
Hello Bjoern Thanks for confirming. Is it right that conda dependency resolution is not supported pre Galaxy v16.01? Best wishes Peter On 15/12/16 10:45, Björn Grüning wrote:
Hi Peter,
Am 15.12.2016 um 11:28 schrieb Peter Briggs:
Dear developers
It looks like some updates to 'devteam'-maintained toolshed tools have dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so their dependencies cannot be automatically installed from the toolshed. Is this correct? I assume that it's part of the move to enforcing conda dependency resolution.
Yes. We really hope we are ready to go for conda, John and Marius have improved the conda support dramatically in the last months.
Thanks, Bjoern
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hi, Am 15.12.2016 um 12:09 schrieb Peter Briggs:
Hello Bjoern
Thanks for confirming. Is it right that conda dependency resolution is not supported pre Galaxy v16.01?
Yes. 16.01 was the first version that was introducing it. To make it clear all older tools will still work, and tool_dependencies will not go away it is just that they are not recommended anymore. Ciao, Bjoern
Best wishes
Peter
On 15/12/16 10:45, Björn Grüning wrote:
Hi Peter,
Am 15.12.2016 um 11:28 schrieb Peter Briggs:
Dear developers
It looks like some updates to 'devteam'-maintained toolshed tools have dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so their dependencies cannot be automatically installed from the toolshed. Is this correct? I assume that it's part of the move to enforcing conda dependency resolution.
Yes. We really hope we are ready to go for conda, John and Marius have improved the conda support dramatically in the last months.
Thanks, Bjoern
Best wishes
Peter
participants (2)
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Björn Grüning -
Peter Briggs