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shed_lint --tools of a suite lints the same tools multiple times #564

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nsoranzo opened this Issue Sep 16, 2016 · 2 comments

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nsoranzo commented Sep 16, 2016

All tool XML files are linted once for each repository in the suite.

$ planemo shed_lint --tools --report_level warn /opt/nsoranzo_tools-iuc/tools/biom_format/
Linting repository /opt/nsoranzo_tools-iuc/tools/biom_format
+Linting tool /opt/nsoranzo_tools-iuc/tools/biom_format/biom_add_metadata.xml
+Linting tool /opt/nsoranzo_tools-iuc/tools/biom_format/biom_convert.xml
Linting repository /opt/nsoranzo_tools-iuc/tools/biom_format
+Linting tool /opt/nsoranzo_tools-iuc/tools/biom_format/biom_add_metadata.xml
+Linting tool /opt/nsoranzo_tools-iuc/tools/biom_format/biom_convert.xml
Linting repository /opt/nsoranzo_tools-iuc/tools/biom_format
+Linting tool /opt/nsoranzo_tools-iuc/tools/biom_format/biom_add_metadata.xml
+Linting tool /opt/nsoranzo_tools-iuc/tools/biom_format/biom_convert.xml

@nsoranzo nsoranzo added the bug label Sep 16, 2016

@peterjc peterjc added the linting label Sep 23, 2016

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shiltemann commented Oct 19, 2016

upvote from me - for mothur it triggers linting of all 125 tools 125 times, making it hard to complete the travis testing within the max build time

@shiltemann shiltemann referenced this issue Nov 7, 2016

Merged

Mothur fixes #967

7 of 7 tasks complete
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nsoranzo commented Feb 2, 2017

And within the log file size limit.

jmchilton added a commit to jmchilton/planemo that referenced this issue Feb 6, 2017

Lint only realized tools during shed linting.
Prevents each tool for being linted for every resolved repository and fixes galaxyproject#564.

Sorry about that.
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