Mercurial > repos > fubar > edger_test

changeset 4:dea65c85afb4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Wed, 12 Jun 2013 03:45:24 -0400 (2013-06-12)
parents e22b0320a4ff
children 06e51c47590d
files rgedgeR/rgedgeRpaired.xml rgedgeR/tool_dependencies.xml rgedgeR/tool_dependencies.xml~
diffstat 3 files changed, 9 insertions(+), 52 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeR/rgedgeRpaired.xml	Wed Jun 12 03:02:29 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Wed Jun 12 03:45:24 2013 -0400
@@ -1,5 +1,11 @@
-<tool id="rgedgeRpaired" name="edgeR paired" version="0.18">
-  <description>2 level Anova for counts</description>
+<tool id="rgedgeRpaired" name="edgeR" version="0.18">
+  <description>1 or 2 level models for count data</description>
+  <requirements>
+      <requirement type="package" version="6.2">">name=package_readline_6_2</requirement>
+      <requirement type="package" version="3.0.1">">name=package_R</requirement>
+      <requirement type="package" version="2.12">">name=package_BioCBasics</requirement>
+  </requirements>
+  
   <command interpreter="python">
      rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "edgeR" 
     --output_dir "$html_file.files_path" --output_html "$html_file" --output_tab "$outtab" --make_HTML "yes"
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 03:02:29 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 03:45:24 2013 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="readline" version="6.2">
+    <package name="package_readline_6_2" version="6.2">
         <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="package_R" version="3.0.1">
@@ -18,7 +18,6 @@
                     <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
                     <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
-
                 </action>
             </actions>
         </install>
--- a/rgedgeR/tool_dependencies.xml~	Wed Jun 12 03:02:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-
-<?xml version="1.0"?>
-
-<tool_dependency>
-<!--
-blame Boris - Ross stole it from his old 2.15 one
--->
-    <package name="readline" version="6.2">
-        <repository  name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-    <package name="package_R" version="3.0.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="readline" version="6.2" />
-                    </repository>
-                </action>
-                <action type="make_directory">$INSTALL_DIR</action>
-                <action type="shell_command">./configure --with-blas --with-lapack --enable-R-shlib --with-readline=no --with-x=no --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
-
-                </action>
-            </actions>
-        </install>
-        <readme>R is a free software environment for statistical computing and graphics
-                WARNING: See custom compilation options above
-                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
-                Added Bioc basics too
-       </readme>
-    </package>
-    <package name="package_BioCBasics" version="2.12">
-        <install version="1.0">
-            <actions>
-                <action type="shell_command">$INSTALL_DIR/lib/R/bin/R CMD BATCH installBioC.R </action>
-            </actions>
-        </install>
-        <readme>R is a free software environment for statistical computing and graphics
-                WARNING: See custom compilation options above
-                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
-                Added Bioc basics via this package installBioC.R script
-       </readme>
-    </package>
-</tool_dependency>