Mercurial > repos > bgruening > deeptools

changeset 2:4762b84d13f5 draft

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Uploaded
author bgruening
date Mon, 05 Aug 2013 10:11:32 -0400
parents 21d563d5f2b2
children 522686bcd5c0
files tool_dependencies.xml
diffstat 1 files changed, 17 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Aug 05 10:09:51 2013 -0400
+++ b/tool_dependencies.xml	Mon Aug 05 10:11:32 2013 -0400
@@ -1,54 +1,41 @@
-    <?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
--->
-
+<?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.18">
-        <repository name="package_samtools_0_1_18" owner="devteam" />
+        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" />
+        <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" />
+        <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" />
+        <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
             <actions>
                 <action type="download_binary">
-                    <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>
+                    <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>
                 </action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
                 </action>
                 <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
-                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
+                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
+                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
                 </action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bigWigInfo</file>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                 </action>
              </actions>
          </install>
@@ -67,10 +54,10 @@
                 </action>
 
                 <action type="set_environment">
-                    <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>
+                    <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>
                     <!-- disable the config file of deepTools -->
-                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
+                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                 </action>
              </actions>
          </install>