Mercurial > repos > bgruening > data_manager_motus
annotate readme.md @ 0:0370fe3cf518 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
author | bgruening |
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date | Thu, 10 Oct 2024 11:00:40 +0000 (2 months ago) |
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0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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1 # Serve locally |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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2 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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3 * Install conda/mamba |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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4 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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5 ``` |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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6 mamba create -n planemo-env python=3.7 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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7 mamba activate planemo-env |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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8 pip install -U planemo |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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9 ``` |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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10 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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11 ## Run DM togehter with tool |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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12 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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13 ``` |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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14 cd <DM-path>/motus-DM |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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15 planemo serve data_manager/motus_db_fetcher.xml <motus_profiler PATH>/motus_profiler.xml --biocontainers --galaxy_root ~/git/galaxy |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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16 ``` |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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17 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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18 ## Check if tool and DM work together |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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19 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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20 In Galaxy go to: |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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21 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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22 * Admin |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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23 * Local Data |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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24 * Check if DM is in **Installed Data Managers** |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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25 * Click it |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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26 * Run the tool with Database type 3.1.0 |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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27 * Admin |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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28 * Data Tables |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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29 * motus_db_versioned |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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30 * Check if new table was made |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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31 * Go to the tool |
0370fe3cf518
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
bgruening
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32 * Check if new table can be found by: `A pre-installed mOTUs database` |