mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
c2ac192750
This is a somewhat substantial reversal in the typical way that the Conda resolver works. Everything related to caching, copying, linking, and building environments on the fly should now only apply if both of the following conditions are met (1) there is more than one requirement tag in a tool and (2) not all of them are resolvable exactly by the Conda resolver. For recipes that don't meet both of these two criteria - the normal case I would suspect going forward - Galaxy will just look for a hashed environment for these requirements built for all the requirements at once whenever the requirements are installed. The new 90% case, such environments should be much less buggy for two primary reasons. - #3299 is solved - in other words Conda is deferred to and if packages have potential conflicts - Conda can choose the right combination of build specifiers to resolve things correctly. - Environments are no longer built on a per-job basis - this means file system problems related to linking and copying aren't really an issue and complexity related to caching can be safely ignored. My guess is we should re-write all the Conda docs to make the other use case seem like a corner case - because hopefully it is now. This commit includes a test tool that wouldn't work without the rewrite I believe.
18 lines
708 B
XML
18 lines
708 B
XML
<tool id="mulled_example_conflict" name="mulled_example_conflict" version="0.1.0">
|
|
<!-- Tool can't be resolved with older style Conda resolution - all requirements
|
|
must be installed together to ensure there is no conflict. -->
|
|
<command detect_errors="exit_code"><![CDATA[
|
|
lumpy 2>&1 | grep -q structural
|
|
]]></command>
|
|
<requirements>
|
|
<requirement type="package" version="0.2.12">lumpy-sv</requirement>
|
|
<requirement type="package" version="1.11.2">numpy</requirement>
|
|
</requirements>
|
|
<inputs>
|
|
<param name="input1" type="text" value="The value" />
|
|
</inputs>
|
|
<outputs>
|
|
<data name="out_file1" format="txt" />
|
|
</outputs>
|
|
</tool>
|