Enable Galaxy outputs_to_working_directory by default#1199
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nsoranzo merged 5 commits intogalaxyproject:masterfrom May 16, 2022
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Enable Galaxy outputs_to_working_directory by default#1199nsoranzo merged 5 commits intogalaxyproject:masterfrom
outputs_to_working_directory by default#1199nsoranzo merged 5 commits intogalaxyproject:masterfrom
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most importantly this will set the galaxy dir and its files dir to read only. which allows planemo test to find cases of tools that write into galaxy's files dir. see also here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483
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nsoranzo
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outputs_to_working_directory by default
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because a .fai is written next to it leads to a failing ci job due to galaxyproject/planemo#1199
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* allow 4 diff for bam files an additional diff line is due to more processors used xref #4490 * link fasta file because a .fai is written next to it leads to a failing ci job due to galaxyproject/planemo#1199
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most importantly this will set the galaxy dir and its files dir to read only (for dockerized testing). which allows planemo test to find cases of tools that write into galaxy's files dir.
see also here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483
related: #1190