Mercurial > repos > iuc > package_mothur_1_36_1

annotate tool_dependencies.xml @ 0:c4cbfb49f1b6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
author iuc
date Mon, 01 Aug 2016 14:34:05 -0400
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c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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1 <?xml version="1.0"?>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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2 <tool_dependency>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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3 <package name="mothur" version="1.36.1">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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4 <install version="1.0">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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5 <actions>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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6 <action sha256sum="dfdc486b24d14d776d45df9d523e62a49332ff0e3def4e0bb95cfbe369638f22" type="download_by_url">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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7 <action type="set_environment_for_install">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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8 <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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9 <package name="legacy_blast" version="2.2.22" />
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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10 </repository>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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11 <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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12 <package name="boost" version="1.57" />
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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13 </repository>
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14 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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15 <package name="zlib" version="1.2.8" />
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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16 </repository>
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17 </action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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18 <action type="shell_command">chmod u+x source/uchime_src/mk</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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19 <action type="shell_command">
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20 test $(uname) = Linux &amp;&amp;
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21 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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22 true
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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23 </action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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24 <action type="shell_command">sed -i.bak -e 's/\ \ \ \ /\t/g' source/makefile;</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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25 <action type="shell_command">sed -i.bak -e '141d;151d;152d' source/makefile;</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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26 <action type="shell_command">sed -i.bak -e 's/fortranSource//g' source/makefile;</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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27 <action type="shell_command">sed -i.bak -e 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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28 <action type="shell_command">sed -i.bak -e 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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29
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30 <action type="shell_command">cd source; make -j 2;</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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31 <action type="move_file">
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32 <source>mothur</source>
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33 <destination>$INSTALL_DIR/bin</destination>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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34 </action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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35 <action type="move_file">
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36 <source>source/uchime</source>
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37 <destination>$INSTALL_DIR/bin</destination>
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38 </action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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39 <action type="set_environment">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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41 </action>
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42 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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43 <action type="change_directory">$INSTALL_DIR/bin</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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44 <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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45 </actions>
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46 </install>
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47 <readme>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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48 *Authors &amp; Contacts*
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49 Jim Johnson
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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50 Peter Briggs
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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51 Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
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52 Kevin Chen | Agriculture and Agri-Foods Canada
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53
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54 *Description*
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55
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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56 The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools. In addition, it downloads and builds the Mothur binaries.
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57
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58 Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.
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59
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60 These links provide information for building the Mothur package in most environments.
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61
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62 http://www.mothur.org/wiki/Download_mothur
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63
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64 http://www.mothur.org/wiki/Installation
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65 http://www.mothur.org/wiki/Makefile_options
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66
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67 *Requirements*
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68
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69 - build tools (make, C libraries, GCC)
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70 - libncurses-dev(el)
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71 - simplejson (python library)
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72 </readme>
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73 </package>
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74 <package name="legacy_blast" version="2.2.22">
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75 <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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76 </package>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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77 <package name="boost" version="1.57">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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78 <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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79 </package>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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80 <package name="zlib" version="1.2.8">
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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81 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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82 </package>
c4cbfb49f1b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
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83 </tool_dependency>