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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="mothur" version="1.33">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://www.mothur.org/w/images/6/65/Mothur.1.33.3.zip</action>
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7 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
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8 <action type="shell_command">
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9 test $(uname) = Linux &amp;&amp;
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10 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile ||
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11 true
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12 </action>
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13 <action type="shell_command">cd Mothur.source; make -j 2;</action>
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14 <action type="move_file">
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15 <source>Mothur.source/mothur</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="move_file">
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19 <source>Mothur.source/uchime</source>
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20 <destination>$INSTALL_DIR/bin</destination>
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21 </action>
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22 <action type="set_environment">
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23 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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24 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
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25 </action>
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26
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27 <action type="make_directory">$INSTALL_DIR/bin/blast</action>
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28 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
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29 <action type="change_directory">$INSTALL_DIR/bin</action>
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30
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31 <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
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32
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33 </actions>
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34 </install>
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35 <readme>
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36 *Authors &amp; Contacts*
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37 Jim Johnson
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38 Peter Briggs
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39 Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
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40 Kevin Chen | Agriculture and Agri-Foods Canada
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41
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42 *Description*
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43
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44 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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45
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46 Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.
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47
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48 These links provide information for building the Mothur package in most environments.
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49
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50 http://www.mothur.org/wiki/Download_mothur
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51
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52 http://www.mothur.org/wiki/Installation
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53 http://www.mothur.org/wiki/Makefile_options
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54
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55 *Requirements*
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56
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57 - build tools (make, C libraries, GCC)
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58 - libncurses-dev(el)
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59 - simplejson (python library)
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60 </readme>
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61 </package>
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62 <package name="blast" version="2.2.26">
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63 <repository
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64 name="package_blast_2_2_26"
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65 owner=""
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66 changeset_revision=""
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67 toolshed=""
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68 prior_installation_required="True"/>
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69 </package>
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70
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71 </tool_dependency>
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72