Mercurial > repos > morinlab > package_expands_1_7_2

comparison tool_dependencies.xml @ 1:b5ab09203060 draft default tip

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author morinlab
date Sun, 04 Dec 2016 17:31:48 -0500
parents 47e78ffd147e
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0:47e78ffd147e 1:b5ab09203060
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R" version="3.1.2"> 3
4 <install version="1.0"> 4 <!-- R -->
5 <actions_group> 5 <package name="R" version="3.1.2">
6 <actions architecture="x86_64" os="linux"> 6 <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
7 <action sha256sum="586dde39d6821bcc5079004450f5d19f836a26d4554083c7add3933f071451e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.1.2_linux_x64.tar.gz</action> 7 </package>
8 <action type="move_directory_files"> 8
9 <source_directory>.</source_directory> 9 <!-- Morinlab scripts with EXPANDS wrapper script -->
10 <destination_directory>$INSTALL_DIR</destination_directory> 10 <package name="morinlab_scripts" version="14.2">
11 </action> 11 <repository changeset_revision="b88b230de028" name="package_morinlab_scripts_14_2" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
12 <action type="set_environment"> 12 </package>
13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> 13
14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> 14 <!-- EXPANDS and other R packages -->
15 </action> 15 <package name="expands" version="1.7.2">
16 </actions> 16
17 <actions> 17 <install version="1.0">
18 <action sha256sum="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a" type="download_by_url">https://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action> 18 <actions>
19 <package name="readline" version="6.2"> 19
20 <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 20 <action type="set_environment_for_install">
21 </package> 21 <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
22 <package name="libpng" version="1.6.7"> 22 <package name="R" version="3.1.2" />
23 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 23 </repository>
24 </package> 24 </action>
25 <package name="cairo" version="1.12.14"> 25
26 <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 26 <action type="shell_command">R CMD javareconf -e</action>
27 </package> 27
28 <package name="pixman" version="0.32.4"> 28 <action type="setup_r_environment">
29 <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 29 <repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
30 </package> 30 <package name="R" version="3.1.2" />
31 <package name="freetype" version="2.5.2"> 31 </repository>
32 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 32 <package>https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz</package>
33 </package> 33 <package>https://cran.r-project.org/src/contrib/mclust_5.2.tar.gz</package>
34 <package name="ncurses" version="5.9"> 34 <package>https://cran.r-project.org/src/contrib/Archive/nnet/nnet_7.3-11.tar.gz</package>
35 <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 35 <package>https://cran.r-project.org/src/contrib/flexmix_2.3-13.tar.gz</package>
36 </package> 36 <package>https://cran.r-project.org/src/contrib/Archive/nlme/nlme_3.1-122.tar.gz</package>
37 <package name="fontconfig" version="2.11.1"> 37 <package>https://cran.r-project.org/src/contrib/ape_3.5.tar.gz</package>
38 <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 38 <package>https://cran.r-project.org/src/contrib/permute_0.9-0.tar.gz</package>
39 </package> 39 <package>https://cran.r-project.org/src/contrib/moments_0.14.tar.gz</package>
40 <action type="set_environment_for_install"> 40 <package>https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz</package>
41 <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 41 <package>https://cran.r-project.org/src/contrib/argparser_0.4.tar.gz</package>
42 <package name="readline" version="6.2" /> 42 <package>https://cran.r-project.org/src/contrib/matlab_1.0.2.tar.gz</package>
43 </repository> 43 <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
44 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 44 <package>https://cran.r-project.org/src/contrib/Archive/digest/digest_0.6.9.tar.gz</package>
45 <package name="libpng" version="1.6.7" /> 45 <package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package>
46 </repository> 46 <package>https://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.12.5.tar.gz</package>
47 <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 47 <package>https://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.3.tar.gz</package>
48 <package name="cairo" version="1.12.14" /> 48 <package>https://cran.r-project.org/src/contrib/Archive/stringi/stringi_1.0-1.tar.gz</package>
49 </repository> 49 <package>https://cran.r-project.org/src/contrib/Archive/stringr/stringr_0.6.2.tar.gz</package>
50 <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 50 <package>https://cran.r-project.org/src/contrib/Archive/reshape2/reshape2_1.4.tar.gz</package>
51 <package name="pixman" version="0.32.4" /> 51 <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
52 </repository> 52 <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package>
53 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 53 <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package>
54 <package name="freetype" version="2.5.2" /> 54 <package>https://cran.r-project.org/src/contrib/Archive/munsell/munsell_0.4.tar.gz</package>
55 </repository> 55 <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
56 <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 56 <package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.3.0.tar.gz</package>
57 <package name="ncurses" version="5.9" /> 57 <package>https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz</package>
58 </repository> 58 <package>https://cran.r-project.org/src/contrib/ggrepel_0.5.tar.gz</package>
59 <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> 59 <package>https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz</package>
60 <package name="fontconfig" version="2.11.1" /> 60 <package>https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz</package>
61 </repository> 61 <package>https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz</package>
62 </action> 62 <package>https://cran.r-project.org/src/contrib/Archive/DBI/DBI_0.4-1.tar.gz</package>
63 <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action> 63 <package>https://cran.r-project.org/src/contrib/Archive/R6/R6_2.1.1.tar.gz</package>
64 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> 64 <package>https://cran.r-project.org/src/contrib/Archive/BH/BH_1.60.0-1.tar.gz</package>
65 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> 65 <package>https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz</package>
66 </actions> 66 <package>https://cran.r-project.org/src/contrib/expands_1.7.2.tar.gz</package>
67 <action type="set_environment"> 67 </action>
68 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> 68 </actions>
69 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable> 69
70 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable> 70 </install>
71 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable> 71
72 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable> 72 </package>
73 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> 73 <readme>
74 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> 74 Expanding Ploidy and Allele Frequency on Nested Subpopulations (EXPANDS) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome-sequencing input data.
75 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> 75 </readme>
76 <!-- Include library with local rJava installation -->
77 <environment_variable action="prepend_to" name="R_LIBS">/usr/lib/R/site-library</environment_variable>
78 <!-- Set JAVA_HOME & LD_LIBRARY_PATH -->
79 <environment_variable action="set_to" name="JAVA_HOME">/usr/lib/jvm/java-8-openjdk-amd64/jre</environment_variable>
80 <environment_variable action="set_to" name="LD_LIBRARY_PATH">/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server</environment_variable>
81 <!-- Set FONTCONFIG_PATH for R png output -->
82 <environment_variable action="set_to" name="FONTCONFIG_PATH">$INSTALL_DIR/etc/fonts</environment_variable>
83 <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
84 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
85 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
86 <!-- Append java bin to PATH -->
87 <environment_variable action="append_to" name="PATH">$JAVA_HOME/bin</environment_variable>
88 </action>
89 </actions_group>
90 </install>
91 <readme>
92 The precompiled versions of this package were built 2014-12-21.
93 R is a free software environment for statistical computing and graphics.
94 NOTE: See custom compilation options above.
95 </readme>
96 </package>
97 </tool_dependency> 76 </tool_dependency>