Mercurial > repos > iarc > mutspec

comparison tool_dependencies.xml @ 7:eda59b985b1c draft default tip

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author iarc
date Mon, 13 Mar 2017 08:21:19 -0400
parents 46a10309dfe2
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6:46a10309dfe2 7:eda59b985b1c
10 <action type="setup_perl_environment"> 10 <action type="setup_perl_environment">
11 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 11 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
12 <package name="perl" prior_installation_required="True" version="5.18.1" /> 12 <package name="perl" prior_installation_required="True" version="5.18.1" />
13 </repository> 13 </repository>
14 14
15 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
16 <package name="R" version="3.0.1" />
17 </repository>
18
19 <!-- allow downloading and installing an Perl package from cpan.org--> 15 <!-- allow downloading and installing an Perl package from cpan.org-->
20 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/IPC-Run-0.94.tar.gz</package> 16 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/IPC-Run-0.94.tar.gz</package>
21 <package>http://search.cpan.org/CPAN/authors/id/A/AB/ABIGAIL/Regexp-Common-2013031301.tar.gz</package> 17 <package>http://search.cpan.org/CPAN/authors/id/A/AB/ABIGAIL/Regexp-Common-2013031301.tar.gz</package>
22 <package>http://search.cpan.org/CPAN/authors/id/F/FA/FANGLY/Statistics-R-0.33.tar.gz</package>
23 <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.19.tar.gz</package> 18 <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.19.tar.gz</package>
24 <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/Spreadsheet-WriteExcel-2.40.tar.gz</package> 19 <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/Spreadsheet-WriteExcel-2.40.tar.gz</package>
25 <package>http://search.cpan.org/CPAN/authors/id/D/DL/DLUX/Parallel-ForkManager-0.7.5.tar.gz</package> 20 <package>http://search.cpan.org/CPAN/authors/id/D/DL/DLUX/Parallel-ForkManager-0.7.5.tar.gz</package>
21 <package>http://search.cpan.org/CPAN/authors/id/G/GR/GROMMEL/Math-Round-0.06.tar.gz</package>
26 </action> 22 </action>
27 <action type="set_environment"> 23 <action type="set_environment">
28 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> 24 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
29 </action> 25 </action>
30 </actions> 26 </actions>
32 </package> 28 </package>
33 29
34 <package name="perl" version="5.18.1"> 30 <package name="perl" version="5.18.1">
35 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 31 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
36 </package> 32 </package>
37 33
38 <package name="weblogo" version="3.3"> 34 <!-- package_weblogo_3_3 has broken link in main Galaxy toolshed (February 2017) -->
39 <repository changeset_revision="648e4b32f15c" name="package_weblogo_3_3" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 35 <package name="weblogo" version="3.5">
36 <install version="1.0">
37 <actions>
38 <action type="download_by_url">https://github.com/WebLogo/weblogo/archive/master.zip</action>
39 <!-- Use screen instead of printer to work around a color bug in ghostscript. -->
40 <action type="shell_command">sed -i.bak 's#"-dPDFSETTINGS=/printer",#"-dPDFSETTINGS=/screen",#' weblogolib/__init__.py</action>
41 <action type="move_directory_files">
42 <source_directory>.</source_directory>
43 <destination_directory>$INSTALL_DIR</destination_directory>
44 </action>
45 <action type="set_environment">
46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
47 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
48 </action>
49 </actions>
50 </install>
51 <readme />
40 </package> 52 </package>
41 53
42 <package name="numpy" version="1.9"> 54 <package name="numpy" version="1.9">
43 <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 55 <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
44 </package> 56 </package>
45 57
46 <package name="R" version="3.1.2"> 58 <package name="R" version="3.2.1">
47 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 59 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
48 </package> 60 </package>
49 61
62 <!-- package_R_3_2_1 doesn't load fontconfig, load it manually -->
63 <package name="fontconfig" version="2.11.1">
64 <repository changeset_revision="d88d844df0cb" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
65 </package>
66
50 <package name="mutspec" version="0.1"> 67 <package name="mutspec" version="0.1">
51 <repository changeset_revision="63cc1719e1aa" name="package_r_mutspec_0_1" owner="iarc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 68 <repository changeset_revision="47d4bc32a67c" name="package_r_mutspec_0_1" owner="iarc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
52 </package> 69 </package>
53 70
54 </tool_dependency> 71 </tool_dependency>