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comparison tool_dependencies.xml @ 1:0bce36ee6bf2

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Edit tpp_gui.pl to change from CGI deprecated endform to end_form
author Jim Johnson <jj@umn.edu>
date Fri, 03 Oct 2014 07:59:16 -0500
parents aad4e1a162c5
children aa519f1dda68
comparison
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0:aad4e1a162c5 1:0bce36ee6bf2
39 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action> 39 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action>
40 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action> 40 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action>
41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action> 41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action>
42 <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action> 42 <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action>
43 43
44 <!-- Change deprecated CGI endform to end_form -->
45 <action type="shell_command">sed -i.orig 's/endform/end_form/' TPP-4.6.3/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl</action>
46
44 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action> 47 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
45 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action> 48 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
46 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action> 49 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
47 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action> 50 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
48 51