Mercurial > repos > wolma > mimodd

changeset 18:2742ad4d1608 draft

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rebase on package_python_3_4_lean
author wolma
date Tue, 26 Apr 2016 11:21:43 -0400
parents b658c34ee3fd
children 8f108b41a149
files tool_dependencies.xml
diffstat 1 files changed, 20 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Apr 26 07:03:26 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 26 11:21:43 2016 -0400
@@ -9,8 +9,8 @@
   <package name="readline" version="6.3">
     <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="python3" version="3.4.1">
-    <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="python3" version="3.4">
+    <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
     
   <package name="mimodd" version="0.1.7.2">
@@ -18,8 +18,8 @@
       <actions>
       <!-- prepare a python3 venv to install into -->
         <action type="set_environment_for_install">
-          <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
-            <package name="python3" version="3.4.1" />
+          <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="python3" version="3.4" />
           </repository>
         </action>
         <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
@@ -27,9 +27,23 @@
              accidental use by Galaxy, MiModD uses python3 explicitly -->
         <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
         <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action>
-        
+
+      <!-- download and install setuptools (required to install rpy2) -->
+        <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
+        <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
+        <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
+        <action type="shell_command">python3 setup.py install</action>
+        <action type="change_directory">$TMP_WORK_DIR</action>
+
+      <!-- download and install six (required by rpy2) -->
+        <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
+        <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
+        <action type="change_directory">six-1.9.0</action>
+        <action type="shell_command">python3 setup.py install</action>
+        <action type="change_directory">$TMP_WORK_DIR</action>
+
       <!-- download and install rpy2 -->
-        <action type="download_file" sha256sum="beb3445cfc3a0f9a36df7de6489d2a488a5ac113c471c448e46e6d9c47cb7840">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
+        <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
         <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
         <action type="change_directory">rpy2-2.7.5</action>
         <action type="set_environment_for_install">