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[17.01] More careful inspection of fixes for MAF tools requiring Galaxy. #3935

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merged 1 commit into from May 2, 2017

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commented Apr 14, 2017

Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934.

More careful inspection of fixes for MAF tools requiring Galaxy.
Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934.

@jmchilton jmchilton added this to the 17.05 milestone Apr 14, 2017

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commented Apr 19, 2017

@jmchilton What about the bx imports? It seems to me that all maf tools should have a requirement on bx-python to properly work, especially the ones not on this list.

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commented Apr 27, 2017

maf_limit_size was removed from the list - its Python file imports are as follows:

from __future__ import print_function

import sys

import bx.align.maf

Since it doesn't import galaxy - I don't think it needs to be in the list. Galaxy's dependencies such as bx are still exposed to tools. A lot more would break I think if bx were to disappear.

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commented May 2, 2017

I'll investigate the bx-python requirement issue separately.

@nsoranzo nsoranzo merged commit de46a0e into galaxyproject:release_17.01 May 2, 2017

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