diff tool_dependencies.xml @ 1:21d563d5f2b2 draft

Uploaded

--- a/tool_dependencies.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/tool_dependencies.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,53 +1,63 @@
-<?xml version="1.0"?>
+    <?xml version="1.0"?>
+<!--
+
+    <requirement type="package">deepTools</requirement>
+    <requirement type="python-module">deepTools</requirement> 
+    <requirement type="python-module">matplotlib</requirement> -> toolshed
+    <requirement type="python-module">argsparse</requirement> -> is in python 2.7 or?
+    <requirement type="python-module">itertools</requirement> -> is in standard python?
+    <requirement type="python-module">pysam</requirement> -> is also shipped with galaxy
+    <requirement type="python-module">numpy</requirement> -> toolshed
+    <requirement type="python-module">pylab</requirement> -> scipy toolshed
+    <requirement type="python-module">bx.intervals.io</requirement> -> bx-python is shipped with galaxy afaik
+-->
+
 <tool_dependency>
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_samtools_0_1_18" owner="devteam" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" />
     </package>
 
-
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
             <actions>
                 <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
+                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
+                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
+                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
+                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
                 </action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
                 </action>
                 <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
+                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
+                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
                 </action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bigWigInfo</file>
                 </action>
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
              </actions>
          </install>
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-
-    <package name="deepTools" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">
+    <package name="deepTools" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">
         <install version="1.0">
             <actions>
-
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
                 <action type="shell_command">git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
@@ -57,8 +67,10 @@
                 </action>
 
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="append_to" >$INSTALL_DIR/lib/python</environment_variable>
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
                 </action>
              </actions>
          </install>