# HG changeset patch
# User jjohnson
# Date 1413295610 14400
# Node ID b9b48eb563d1ad4906558525250e37e647240f04

Imported from capsule None

diff -r 000000000000 -r b9b48eb563d1 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 14 10:06:50 2014 -0400
@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="numpy" version="1.7.1">
+      <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="cython" version="0.20.1">
+      <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="cistrome" version="2014-09-29">
+      <install version="1.0">
+          <actions>
+              <action type="shell_command">hg clone https://bitbucket.org/jjohnson/cistrome-applications-harvard cistrome</action>
+                <action type="shell_command">hg update -d 2014-09-29</action>
+                <action type="shell_command">cd cistrome-extra-apps &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
+                <action type="shell_command">cd published-packages/CEAS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
+                <action type="shell_command">cd published-packages/MA2C &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
+                <!--  needs numpy  -->
+                <action type="set_environment_for_install">
+                  <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                      <package name="numpy" version="1.7.1" />
+                    </repository>
+                </action>
+                <action type="shell_command">cd published-packages/MACS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
+                <action type="shell_command">cd published-packages/MAT &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
+                <action type="shell_command">cd published-packages/NPS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
+                <!--  needs numpy Cython  -->
+                <action type="set_environment_for_install">
+                  <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                      <package name="cython" version="0.20.1" />
+                    </repository>
+                </action>
+                <action type="shell_command">
+                   export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                   cd mdseqpos &amp;&amp; 
+                   sed "s#/data/static_libraries/assembly/#$INSTALL_DIR/assembly/#" lib/settings.py.example &gt; lib/settings.py &amp;&amp; 
+                   sed -i".tmp" "s#NUMPY_PATH = numpy#global NUMPY_PATH; NUMPY_PATH = numpy#" setup.py  &amp;&amp;
+                   python setup.py install --home=$INSTALL_DIR
+                </action>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <!--  this includes CistromeAP  -->
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib64/python</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Installs the cistrome applications code from https://bitbucket.org/cistrome/cistrome-applications-harvard
+  ( branch for genome_dir option to override settings.py  https://bitbucket.org/jjohnson/cistrome-applications-harvard )
+Runtime dependencies: bx-python, biopython, PIL, jinja2, MySQLdb
+        </readme>
+    </package>
+</tool_dependency>