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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
author iuc
date Tue, 13 Sep 2022 09:08:55 +0000
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40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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1 If Galaxy is configured such that outputs are written to the job working dir
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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2 the admin needs to perform one manual step to make the databases useable.
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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3 This is because DRAM creates a configuration file during installation, but the
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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4 file is written before the Galaxy job finishes, so the database locations are
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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5 relative to the job working directory instead of the configured
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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6 GALAXY_DATA_MANAGER_DATA_PATH.
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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7
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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8 It may be more ideal to perform this task as a second step in the data manager
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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9 tool, but DRAM will not allow the configuration file to be updated to point to
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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10 locations unless the databases exist in those locations. But the data manager
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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11 tool moves the databases to these locations as its last step, making it
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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12 impossible to update the DRAM configuration file as a second step of that tool.
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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14 See
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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15 https://github.com/WrightonLabCSU/DRAM/wiki/5.-Managing%2C-updating-or-moving-a-DRAM-installation-and-databases
40c8fc0a2bb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
iuc
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16 for details.