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comparison tool_dependencies.xml @ 13:f0b3871cb869 draft

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author wolma
date Mon, 25 Apr 2016 17:27:25 -0400
parents ac3eac581b83
children 5e9c1c67716b
comparison
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12:c2c70edb70eb 13:f0b3871cb869
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="zlib" version="1.2.8"> 3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="R" version="3.2.1">
7 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="readline" version="6.2">
10 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 11 </package>
6 <package name="python3" version="3.4.1"> 12 <package name="python3" version="3.4.1">
7 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package> 14 </package>
9 15
10 <package name="mimodd" version="0.1.7.2"> 16 <package name="mimodd" version="0.1.7.2">
11 <install version="1.0"> 17 <install version="1.0">
12 <actions> 18 <actions>
13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> 19 <!-- prepare a python3 venv to install into -->
14 <action type="set_environment_for_install"> 20 <action type="set_environment_for_install">
15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> 21 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
16 <package name="python3" version="3.4.1" /> 22 <package name="python3" version="3.4.1" />
17 </repository> 23 </repository>
18 </action> 24 </action>
25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
26 <!-- remove the plain python symlink from the venv to avoid its
27 accidental use by Galaxy, MiModD uses python3 explicitly -->
28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
29 <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action>
30
31 <!-- download and install rpy2 -->
32 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_by_url">
33 https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz
34 </action>
35 <action type="set_environment_for_install">
36 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
37 <package name="readline" version="6.2" />
38 </repository>
39 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
40 <package name="R" version="3.2.1" />
41 </repository>
42 </action>
43 <action type="shell_command">
44 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
45 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
46 python3 setup.py install
47 </action>
48 <action type="change_directory">$TMP_WORK_DIR</action>
49
50 <!-- download and install MiModD -->
51 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
19 <action type="set_environment_for_install"> 52 <action type="set_environment_for_install">
20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> 53 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="zlib" version="1.2.8" /> 54 <package name="zlib" version="1.2.8" />
22 </repository> 55 </repository>
23 </action> 56 </action>
24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
25 <!-- remove the plain python symlink from the venv to avoid its
26 accidental use by Galaxy, MiModD uses python3 explicitly -->
27 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
28 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> 57 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
29 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> 58 <action type="shell_command">python3 setup.py install</action>
30 <!-- make MiModD's wrapped binaries executable --> 59 <!-- make MiModD's wrapped binaries executable -->
31 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action> 60 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
32 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> 61 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
33 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action> 62 <action type="shell_command">python3 -m MiModD.__first_run__</action>
34 63
35 <action type="set_environment"> 64 <action type="set_environment">
36 <!-- make the mimodd entry script discoverable --> 65 <!-- make the mimodd entry script discoverable -->
37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> 66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
38 <!-- clear $PYTHONPATH and $PYTHONHOME --> 67 <!-- clear $PYTHONPATH and $PYTHONHOME -->
39 <environment_variable action="set_to" name="PYTHONPATH" /> 68 <environment_variable action="set_to" name="PYTHONPATH" />
40 <environment_variable action="set_to" name="PYTHONHOME" /> 69 <environment_variable action="set_to" name="PYTHONHOME" />
41 <!-- propagate $LD_LIBRARY_PATH --> 70 <!-- propagate $LD_LIBRARY_PATH -->
42 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable> 71 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
43 </action> 72 </action>
44
45 73
46 </actions> 74 </actions>
47 </install> 75 </install>
48 <readme> 76 <readme>
49 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs 77 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs