Mercurial > repos > lparsons > htseq_count

diff tool_dependencies.xml @ 20:3b3601a2a7c7 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
author lparsons
date Mon, 22 Jun 2015 17:01:05 -0400
parents d5edaf8dc974
children a6dcb86af112
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line diff
--- a/tool_dependencies.xml	Mon Oct 13 14:07:30 2014 -0400
+++ b/tool_dependencies.xml	Mon Jun 22 17:01:05 2015 -0400
@@ -1,40 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
 
-    <package name="numpy" version="1.7.1">
-        <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="pysam" version="0.7.7">
-        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="htseq" version="0.6.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="numpy" version="1.7.1" />
-                   </repository>
-                </action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
-                <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
-        </readme>
+        <repository changeset_revision="5b3da3e3543d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 
 </tool_dependency>