Mercurial > repos > s-kaufmann > synteny_mapper

comparison tool_dependencies.xml @ 12:3d74b350ec59 draft

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author s-kaufmann
date Fri, 15 Aug 2014 09:43:10 -0400
parents a6c5e5a41025
children acb6cae8bfec
comparison
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11:833d7d8ce458 12:3d74b350ec59
25 <readme> 25 <readme>
26 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed. 26 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
27 </readme> 27 </readme>
28 </package> 28 </package>
29 29
30 <package name="R_3_0_1" version="3.0.1"> 30 <set_environment version="1.0">
31 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
32 </set_environment>
33 <package name="readline" version="6.2">
34 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
35 </package>
36 <package name="ncurses" version="5.9">
37 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
38 </package>
39 <package name="libpng" version="1.6.7">
40 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
41 </package>
42 <package name="R_3_0_2" version="3.0.2">
31 <install version="1.0"> 43 <install version="1.0">
32 <actions> 44 <actions>
33 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action> 45 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
34 <!--<action type="set_environment_for_install"> 46 <action type="set_environment_for_install">
35 <repository name="package_readline_6_2" owner="iuc"> 47 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
36 <package name="readline" version="6.2" /> 48 <package name="readline" version="6.2" />
37 </repository> 49 </repository>
38 </action>--> 50 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
51 <package name="ncurses" version="5.9" />
52 </repository>
53 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
54 <package name="libpng" version="1.6.7" />
55 </repository>
56 </action>
39 57
40 <action type="shell_command"> 58 <action type="shell_command">
41 ./configure --with-readline=no --enable-R-shlib --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR/bin/ --datarootdir=$INSTALL_DIR/share/ 59 ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
42 </action> 60 </action>
61
43 <action type="shell_command">make</action> 62 <action type="shell_command">make</action>
44 <action type="shell_command">make install</action> 63 <action type="shell_command">make install</action>
45 <action type="set_environment"> 64 <action type="set_environment">
46 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> 65 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
47 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> 66 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
51 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable> 70 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
52 </action> 71 </action>
53 </actions> 72 </actions>
54 </install> 73 </install>
55 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme> 74 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
56 </package> 75 </package>
57 76
58 </tool_dependency> 77 </tool_dependency>