annotate macros.xml @ 1:f415e44e71de draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
author gga
date Mon, 03 Apr 2023 15:01:52 +0000
parents 22f22c3e81bf
children 5a6050937cb9
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
1
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5 <requirement type="package" version="@TOOL_VERSION@">genoboo</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9
1
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10 <token name="@TOOL_VERSION@">0.4.1</token>
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11 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
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12
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13 <xml name="citation">
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14 <citations>
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15 <citation type="doi">10.1093/bioinformatics/btz491</citation>
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16 </citations>
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17 </xml>
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18
1
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19 <xml name="sanitized">
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20 <sanitizer>
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21 <valid initial="string.printable">
f415e44e71de planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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22 <remove value="&apos;"/>
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23 </valid>
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24 <mapping initial="none">
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25 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
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26 <add source="(" target="\("/>
f415e44e71de planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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27 <add source=")" target="\)"/>
f415e44e71de planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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28 </mapping>
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29 </sanitizer>
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30 </xml>
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31
0
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32 <token name="@CONNECT_INFO@">-u admin -p admin --port \$GNB_PORT</token>
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33
22f22c3e81bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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34 <!--
22f22c3e81bf planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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35 This runs GeneNoteBook, and a local mongodb server listening only on a unix socket, created in the work dir.
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36 The bind_ip option is a trick to prevent mongod from opening a TCP socket.
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37 For some unknwon reason, unixSocketPrefix needs an absolute path
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38 -->
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39 <token name="@START_GNB@"><![CDATA[
1
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40 export GNB_PORT="\$(bash '$__tool_directory__/find_free_port.sh')";
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41 export MONGO_URI="\$(pwd | sed 's|/|%2F|g')";
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42 #if $existing
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43 tar -xf '${existing}' mongo_db;
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44 #else
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45 mkdir ./mongo_db/;
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46 #end if
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47 . '$__tool_directory__/launch_gnb.sh';
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48 ]]></token>
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49
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50 <token name="@ZIP_GNB@"><![CDATA[
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51 . '$__tool_directory__/kill_gnb.sh';
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52
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53 ## Zip the mongodb data dir
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54 tar -cvjf '${gnb_db}' mongo_db > /dev/null;
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55
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56 ## Make sure mongodb and GNB are really really stopped even if anything failed before
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57 ## We assume the DRM or container exit will kill any remaining process after that, but who knows.
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58 kill \$GNB_PID &> /dev/null || true ;
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59 kill \$(<"./mongo.pid") &> /dev/null || true ;
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60 ]]></token>
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61 </macros>