# HG changeset patch
# User bgruening
# Date 1381533896 14400
# Node ID 213d82f33fc23a8dc2546e6c7cd7c89e3ae7d2ab
# Parent  e2df6fe8b4472d51a37ab811ffd66c5cedf5681b
Uploaded

diff -r e2df6fe8b447 -r 213d82f33fc2 antismash.xml
--- a/antismash.xml	Fri Oct 11 16:46:08 2013 -0400
+++ b/antismash.xml	Fri Oct 11 19:24:56 2013 -0400
@@ -4,7 +4,8 @@
         <requirement type="package" version="3.0">hmmer</requirement>
         <requirement type="package" version="2.2.28">blast+</requirement>
         <requirement type="package" version="3.8.31">muscle</requirement>
-        <requirement type="package" version="2.0.2">antismash_python_deps</requirement>
+        <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement>
+        <requirement type="package" version="0.1.2">helperlibs</requirement>
         <requirement type="package" version="2.0.2">antismash</requirement>
     </requirements>
     <command>
diff -r e2df6fe8b447 -r 213d82f33fc2 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Oct 11 16:46:08 2013 -0400
+++ b/tool_dependencies.xml	Fri Oct 11 19:24:56 2013 -0400
@@ -9,15 +9,37 @@
     <package name="muscle" version="3.8.31">
         <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="antismash_python_deps" version="2.0.2">
+
+    <package name="helperlibs" version="0.1.2">
         <install version="1.0">
             <actions>
-                <action type="setup_virtualenv">helperlibs==0.1.2
-straight.plugin==1.4.0-post-1</action>
+                <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</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 $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
             </actions>
         </install>
         <readme>
-            AntiSmash python dependencies (helperlibs and straight.plugin)
+            helperlibs python library
+        </readme>
+    </package>
+    <package name="straight.plugin" version="1.4.0-post-1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action>
+                <action type="make_directory">$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 $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            straight.plugin python library
         </readme>
     </package>
     <package name="antismash" version="2.0.2">
@@ -37,7 +59,7 @@
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
                     -->
-                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
@@ -55,7 +77,7 @@
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
                     -->
-                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
@@ -73,7 +95,7 @@
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
                     -->
-                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
@@ -91,7 +113,7 @@
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
                     -->
-                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>