Mercurial > repos > devteam > package_emboss_5_0_0

annotate tool_dependencies.xml @ 8:27daa4034544 draft

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Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
author devteam
date Tue, 10 Dec 2013 14:11:14 -0500
parents 27b61d58dfb4
children 423c17dafd88
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9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
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1 <?xml version="1.0"?>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
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2 <tool_dependency>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
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3 <package name="emboss" version="5.0.0">
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27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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4 <install version="1.0">
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5 <actions_group>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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6 <actions architecture="i386" os="linux">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/emboss/emboss-5.0.0-Linux-i686.tgz</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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8 <action type="move_directory_files">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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12 </actions>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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13 <actions architecture="x86_64" os="linux">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/emboss/emboss-5.0.0-Linux-x86_64.tgz</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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17 <destination_directory>$INSTALL_DIR</destination_directory>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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18 </action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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19 </actions>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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20 <actions architecture="x86_64" os="darwin">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/emboss/emboss-5.0.0-Darwin-x86_64.tgz</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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22 <action type="move_directory_files">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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23 <source_directory>.</source_directory>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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24 <destination_directory>$INSTALL_DIR</destination_directory>
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25 </action>
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26 </actions>
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27 <actions>
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27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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28 <package name="libx11" version="1.5.0">
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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29 <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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30 </package>
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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31 <package name="libxproto" version="7.0.23">
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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32 <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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33 </package>
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34 <package name="libxcb" version="1.9.1">
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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35 <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
27daa4034544 Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.
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36 </package>
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37 <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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38 <action type="set_environment_for_install">
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39 <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
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40 <package name="libx11" version="1.5.0" />
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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41 </repository>
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42 <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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43 <package name="libxproto" version="7.0.23" />
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44 </repository>
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45 <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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46 <package name="libxcb" version="1.9.1" />
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47 </repository>
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48 </action>
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49 <action type="shell_command">
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50 export LDFLAGS="-L$XCB_LIBS -lm"
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51 export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
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52 </action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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53 <action type="shell_command">make &amp;&amp; make install</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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54 <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
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55 <action type="change_directory">PHYLIP-3.6b</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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56 <action type="shell_command">
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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57 export LDFLAGS="-L$XCB_LIBS -lm"
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58 export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
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59 </action>
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60 <action type="shell_command">make &amp;&amp; make install</action>
27b61d58dfb4 Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
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61 </actions>
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62 <action type="set_environment">
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63 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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64 <environment_variable action="set_to" name="EMBOSS_ACDROOT">$INSTALL_DIR/share/EMBOSS/acd</environment_variable>
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65 <environment_variable action="set_to" name="EMBOSS_DATA">$INSTALL_DIR/share/EMBOSS/data</environment_variable>
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66 <environment_variable action="set_to" name="PLPLOT_LIB">$INSTALL_DIR/share/EMBOSS</environment_variable>
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67 </action>
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68 </actions_group>
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69 </install>
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70 <readme>
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71 These links provide information for building the Emboss package in most environments.
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72
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
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73 System requirements
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
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74 http://emboss.sourceforge.net/download/#Requirements
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75
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
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76 Platform-dependent notes
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77 http://emboss.sourceforge.net/download/#Platforms
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78 </readme>
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79 </package>
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80 </tool_dependency>