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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="gnu_coreutils" version="8.25">
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4 <repository changeset_revision="7241ed879fb4" name="package_gnu_coreutils_8_25" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="perl" version="5.18.1">
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7 <install version="1.0">
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8 <actions>
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9 <!-- install perl -->
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10 <action sha256sum="655e11a8ffba8853efcdce568a142c232600ed120ac24aaebb4e6efe74e85b2b" type="download_by_url">
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11 https://depot.galaxyproject.org/software/perl/perl_5.18_src_all.tar.gz
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12 </action>
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13 <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
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14 <action type="make_install" />
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15 <action type="change_directory">..</action>
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16 <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file">
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17 http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz
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18 </action>
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19 <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
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20 <action type="change_directory">local-lib-1.008009</action>
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21 <!-- TODO: Here we need to use the new installed perl binary -->
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22 <!-- Test whether $TMP_WORK_DIR exists (introduced in galaxy release 15.07).
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23 If not, fall back to using mktemp. Should be set to HOME=$TEMP_WORK_DIR in the future. -->
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24 <action type="shell_command">if [ -d "$TMP_WORK_DIR" ] ; then export HOME=$TMP_WORK_DIR ; else export HOME=`mktemp -d` ; fi ; export PATH=$INSTALL_DIR/bin/:$PATH; perl Makefile.PL --bootstrap=$INSTALL_DIR/local-lib/ --no-manpages</action>
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25 <action type="shell_command">make install</action>
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26 <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action>
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27 <action type="change_directory">..</action>
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28 <!-- install cpanminus into our new perl environment -->
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29 <action sha256sum="0b67f5c721259d4185bacdcbc87b835821246fe8ac7ad980d3b1a18ecdd10ff6" type="download_file">
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30 https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm
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31 </action>
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32 <!-- prepending means that the new install perl binary will be used after the pipe -->
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33 <action type="shell_command">if [ -d "$TMP_WORK_DIR" ] ; then export HOME=$TMP_WORK_DIR ; else export HOME=`mktemp -d` ; fi ; unset PERL_MB_OPT PERL_MM_OPT ; export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB ; export PATH=$INSTALL_DIR/bin/:$PATH ; cat cpanm | perl - App::cpanminus</action>
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34 <action type="shell_command">LC_ALL=C sed -i.bak -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action>
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35 <action type="set_environment">
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36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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37 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
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38 <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR</environment_variable>
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39 <environment_variable action="set_to" name="PERL_LOCALLIB_DIR">$INSTALL_DIR/local-lib</environment_variable>
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40 </action>
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41 </actions>
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42 </install>
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43 <readme>
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44 Perl 5 is a highly capable, feature-rich programming language with over 25 years of development.
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45 https://www.perl.org/
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46
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47 This repository contains local-lib and cpanm in addition.
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48 It is recommended to use something like "cpanm --local-lib=$PERL_ROOT_DIR XML::Parser" to install additional perl modules.
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49 </readme>
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50 </package>
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51 </tool_dependency>
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