Mercurial > repos > melissacline > ucsc_xena_platform
annotate xenaAdmin.xml @ 55:421b18a0b659 default tip
update v17 step 2, add xena.jar
| author | jingchunzhu |
|---|---|
| date | Tue, 22 Sep 2015 10:07:51 -0700 |
| parents | 77f5d8cbac77 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="xenaAdmin" name="Xena Administration" version="0.0.2"> |
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77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
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2 <description>Administer the Galaxy-embedded Xena: start, check status, stop, check xena version, backup, restore</description> |
| 0 | 3 <requirements> |
| 4 <requirement type="package" version="1.0">installXena</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 #if $adminAction.actionType == "backup": | |
| 8 xena_backup.py ${adminAction.backupDir} $outfile | |
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9 #else if $adminAction.actionType == "restore": |
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ca4510434eda
Moved the xena delete functionality into xena admin
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parents:
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10 xena_restore.py ${adminAction.restoreDir} $outfile |
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ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
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diff
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11 #else if $adminAction.actionType == "delete": |
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ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
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diff
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12 xena_delete.py ${adminAction.datasetId} $outfile |
| 0 | 13 #else: |
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ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
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14 runXena.py ${adminAction.actionType} $outfile |
| 0 | 15 #end if |
| 16 </command> | |
| 17 <inputs> | |
| 18 <conditional name="adminAction"> | |
| 19 <param format="str" type="select" name = "actionType" label="Action"> | |
| 20 <option value="status">Check Status</option> | |
| 21 <option value="start">Start Xena</option> | |
| 22 <option value="stop">Stop Xena</option> | |
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77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
1
diff
changeset
|
23 <option value="version">Check Current Xena Server Version</option> |
| 0 | 24 <option value="backup">Backup the Xena data to an external directory</option> |
| 25 <option value="restore">Restore data to Xena from an external backup directory</option> | |
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ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
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26 <option value="delete">Delete a dataset from the local Galaxy-embedded Xena</option> |
| 0 | 27 </param> |
| 28 <when value="backup"> | |
| 29 <param label="External Directory" type="text" name="backupDir" value="/tmp/xena_files"/> | |
| 30 </when> | |
| 31 <when value="restore"> | |
| 32 <param label="Backup Directory" type="text" name="restoreDir" value="/tmp/xena_files"/> | |
| 33 </when> | |
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melissacline
parents:
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34 <when value="delete"> |
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ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
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35 <param label="Dataset ID" type="text" name="datasetId"/> |
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ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
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36 </when> |
| 0 | 37 <when value="status"/> |
| 38 <when value="start"/> | |
| 39 <when value="stop"/> | |
|
30
77f5d8cbac77
add functionality to check the version of the current running xena server on the galaxy system
Jing Zhu <jzhu@soe.ucsc.edu>
parents:
1
diff
changeset
|
40 <when value="version"/> |
| 0 | 41 </conditional> |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data format="txt" name="outfile"/> | |
| 45 </outputs> | |
| 46 <help> | |
| 47 | |
| 48 **Xena Administration** | |
| 49 | |
| 50 Administer the Galaxy-embedded Xena by starting it, stopping it or checking its status. If you start Xena, or if you check the status while Xena is running, the output will indicate a URL for the Xena server that you can enter in the Xena Data Hub tool. After you add a new data hub with this URL, and select it, you will be able to see the data from this Xena in the Xena browser. | |
| 51 | |
| 52 With this tool, you can also backup the data from your Galaxy-embedded Xena to an external directory on the same computer, and can restore data from a previous backup into the Xena database. If you wish to restore data, Xena must be running first. | |
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53 |
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melissacline
parents:
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54 Finally, you can use this tool to remove a dataset from the Galaxy-embedded local Xena. Simply indicate the dataset by Dataset ID, which you will find under the Xena Data Pages. |
| 0 | 55 |
| 56 </help> | |
| 57 </tool> | |
| 58 | |
| 59 | |
| 60 |