diff tool_dependencies.xml @ 64:627004611e98 draft

Uploaded

--- a/tool_dependencies.xml	Thu Feb 26 11:04:18 2015 -0500
+++ b/tool_dependencies.xml	Sun Mar 22 13:02:33 2015 -0400
@@ -1,6 +1,93 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.2.1">
+        <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.12.0">
+        <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bx-python" version="0.7.1">
+        <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ucsc_tools" version="0.1">
+        <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="deepTools" version="1.5.9">
-        <repository changeset_revision="ebb8126cb112" name="package_deeptools_1_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.7.7" />
+                    </repository>
+                    <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="0.7.1" />
+                    </repository>
+                    <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                    <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="matplotlib" version="1.2.1" />
+                    </repository>
+                    <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="scipy" version="0.12.0" />
+                    </repository>
+                    <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="samtools" version="0.1.19" />
+                    </repository>
+                    <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ucsc_tools" version="0.1" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
+                    <!-- include samtools into PATH -->
+                    <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
+                    <!-- include numpy -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                    <!-- include matplotlib -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[MATPLOTLIB_LIB_PATH]</environment_variable>
+                    <!-- include scipy -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
+                    <!-- include bx-python -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
+                    <!-- include pysam -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
+                    <!-- include ucsc tools -->
+                    <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
+
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
+                </action>
+             </actions>
+         </install>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
+     </package>
 </tool_dependency>