Mercurial > repos > gga > genenotebook_genenotebook_build
annotate macros.xml @ 8:29eeddd8ea62 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 1429f00733ee24bf2edf56b9fd7ff4ad2dec3f15
author | gga |
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date | Tue, 20 Feb 2024 10:05:05 +0000 |
parents | dfb2bc3aedbd |
children | e98f93ba54cd |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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1 <?xml version="1.0"?> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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2 <macros> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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3 <xml name="requirements"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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4 <requirements> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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5 <requirement type="package" version="@TOOL_VERSION@">genoboo</requirement> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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6 <yield/> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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7 </requirements> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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8 </xml> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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9 |
8
29eeddd8ea62
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 1429f00733ee24bf2edf56b9fd7ff4ad2dec3f15
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10 <token name="@TOOL_VERSION@">0.4.13</token> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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11 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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12 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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13 <xml name="citation"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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14 <citations> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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15 <citation type="doi">10.1093/bioinformatics/btz491</citation> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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16 </citations> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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17 </xml> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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18 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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19 <xml name="sanitized"> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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20 <sanitizer> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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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="'"/> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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23 </valid> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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24 <mapping initial="none"> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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25 <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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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> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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29 </sanitizer> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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30 </xml> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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31 |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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32 <token name="@CONNECT_INFO@">-u admin -p admin --port \$GNB_PORT</token> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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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. |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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36 The bind_ip option is a trick to prevent mongod from opening a TCP socket. |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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37 For some unknwon reason, unixSocketPrefix needs an absolute path |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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38 --> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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39 <token name="@START_GNB@"><![CDATA[ |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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40 export MONGO_URI="\$(pwd | sed 's|/|%2F|g')"; |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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41 #if $existing |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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42 tar -xf '${existing}' mongo_db; |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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43 #else |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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44 mkdir ./mongo_db/; |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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45 #end if |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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46 . '$__tool_directory__/launch_gnb.sh'; |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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47 ]]></token> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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48 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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49 <token name="@ZIP_GNB@"><![CDATA[ |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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50 . '$__tool_directory__/kill_gnb.sh'; |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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51 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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52 ## Zip the mongodb data dir |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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53 tar -cvjf '${gnb_db}' mongo_db > /dev/null; |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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54 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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55 ## Make sure mongodb and GNB are really really stopped even if anything failed before |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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56 ## We assume the DRM or container exit will kill any remaining process after that, but who knows. |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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57 kill \$GNB_PID &> /dev/null || true ; |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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58 kill \$(<"./mongo.pid") &> /dev/null || true ; |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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59 ]]></token> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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60 </macros> |