Mercurial > repos > iuc > package_python_2_7_pybedtools_0_6_9

changeset 0:899ca0558676 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_pybedtools_0_6_9 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:28:43 -0400
parents
children 85fe6cd6aa72
files tool_dependencies.xml
diffstat 1 files changed, 44 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jul 17 14:28:43 2015 -0400
@@ -0,0 +1,44 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="tabix" version="0.2.6">
+        <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bedtools" version="2.22">
+        <repository changeset_revision="960f83563956" name="package_bedtools_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="cython" version="0.20.1">
+        <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="python" version="2.7">
+        <repository changeset_revision="997181c8671c" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pybedtools" version="0.6.9">
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                    <repository changeset_revision="997181c8671c" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                       <package name="python" version="2.7" />
+                    </repository>
+                    <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="cython" version="0.20.1" />
+                    </repository>
+                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
+                    <package>https://github.com/daler/pybedtools/archive/v0.6.9.tar.gz</package>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="PYTHONPATH_PYBEDTOOLS">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="PATH_PYBEDTOOLS">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="PYBEDTOOLS_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling pybedtools requires cython and the gcc compiler.
+            https://github.com/daler/pybedtools
+        </readme>
+    </package>
+</tool_dependency>