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planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
author bgruening
date Wed, 24 Apr 2019 06:11:25 -0400
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2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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1 <?xml version="1.0"?>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2 <macros>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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3 <xml name="inputs_outputs">
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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4 <inputs>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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5 <param format="tabular" help="" label="Input tabular dataset" name="in_file" type="data" />
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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6 <yield />
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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7 </inputs>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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8 <outputs>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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9 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}" />
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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10 </outputs>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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11 </xml>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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12
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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13 <xml name="requirements">
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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14 <requirements>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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15 <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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16 <requirement type="package" version="0.1">pglite</requirement>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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17 </requirements>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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18 </xml>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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20 <token name="@PG_VERSION@">11.2</token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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22 <token name="@HELP_FOOTER@">
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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23 The postgresql tools, are using a postgresql database in user-space. Databases are packed into a tarball and stored in the user-history.
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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24 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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26 <token name="@UNTAR_INFILE@"><![CDATA[
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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27 tar -xjvf '$infile' &&
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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28 export PWD=`pwd` &&
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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29 sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '\$PWD/postgresql/'|" ./postgresql/db/postgresql.conf
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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30 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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31 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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33 <token name="@PG_SETUP@"><![CDATA[
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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34 pglite setup -d ./postgresql &&
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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35 @PG_START@
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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36 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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37 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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39 <token name="@PSQL@"><![CDATA[
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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40 psql "\$(pglite url -d ./postgresql)"
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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41 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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42 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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44 <token name="@STATUS_RUNNING@"><![CDATA[
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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45 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' &&
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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46 pglite status -d ./postgresql &&
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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47 timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done'
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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48 && pglite status -d ./postgresql
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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49 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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50 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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52 <token name="@STOPPED@"><![CDATA[
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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53 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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54 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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55 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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57 <token name="@PG_START@"><![CDATA[
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58 pglite start -d ./postgresql &&
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59 @STATUS_RUNNING@
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60 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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61 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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62
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63 <token name="@PG_STOP@"><![CDATA[
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64 pglite stop -d ./postgresql &&
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65 @STOPPED@
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66 ]]>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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67 </token>
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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69 <token name="@ARCHIVE_DATABASE@"><![CDATA[
2c43bac3579f planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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70 tar -cvjf postgresql_out.tar.bz2 postgresql
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71 ]]>
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72 </token>
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73 <xml name="citations">
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74 <citations></citations>
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75 </xml>
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76 </macros>