Mercurial > repos > peterjc > package_mira_4_9_5

annotate tool_dependencies.xml @ 0:9ac25aeb7c88 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
author peterjc
date Wed, 26 Aug 2015 06:04:08 -0400
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children b758c4e48fa5
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9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
peterjc
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1 <?xml version="1.0"?>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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2 <tool_dependency>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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3 <package name="MIRA" version="4.9.5">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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4 <install version="1.0">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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5 <actions_group>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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6 <!-- Download the binaries for MIRA compatible with 64-bit OSX. -->
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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7 <actions architecture="x86_64" os="darwin">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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8 <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_darwin14.3.0_x86_64_static.tar.bz2</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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9 <action type="move_directory_files">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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10 <source_directory>bin</source_directory>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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11 <destination_directory>$INSTALL_DIR</destination_directory>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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12 </action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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13 </actions>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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14 <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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15 <actions architecture="x86_64" os="linux">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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16 <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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17 <action type="move_directory_files">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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18 <source_directory>bin</source_directory>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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19 <destination_directory>$INSTALL_DIR</destination_directory>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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20 </action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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21 </actions>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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22 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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23 <actions>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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24 <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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25 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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26 <action type="shell_command">uname</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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27 <action type="shell_command">arch</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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28 <action type="shell_command">echo "If pre-compiled MIRA binaries are now available for this, please report this"</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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29 <action type="shell_command">echo "via https://github.com/peterjc/pico_galaxy/issues - thank you!"</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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30 <action type="shell_command">false</action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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31 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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32 </actions>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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33 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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34 <action type="set_environment">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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36 </action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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37 <action type="set_environment">
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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38 <environment_variable action="set_to" name="MIRA4">$INSTALL_DIR</environment_variable>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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39 </action>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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40 </actions_group>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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41 </install>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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42 <readme>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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43 Downloads MIRA v4.9.5 from Sourceforge, requesting Bastien's precompiled binaries
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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44 for 64 bit (x86_64) Linux or Mac OS X. Other platforms where compilation from
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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45 source would be required (e.g. 32 bit Linux) are not supported by this automated
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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46 installation script.
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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47
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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48 http://chevreux.org/projects_mira.html
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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49 http://sourceforge.net/projects/mira-assembler/
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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50
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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51 The environment variable ``$MIRA4`` will point to the folder containing the binaries,
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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52 which is also pre-pended to the``$PATH`` variable.
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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53 </readme>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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54 </package>
9ac25aeb7c88 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit 92d55561cbd4b8fcfd39e3e86e497d3e2a05a2f2
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55 </tool_dependency>