Mercurial > repos > kevyin > meme_chip

changeset 12:4e760ac2459a draft

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Uploaded
author kevyin
date Mon, 12 Nov 2012 18:09:08 -0500
parents 69a166a7c178
children 4bd96f3f1f48
files README meme_chip_wrapper.xml tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 4 files changed, 27 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/README	Wed Nov 07 00:39:54 2012 -0500
+++ b/README	Mon Nov 12 18:09:08 2012 -0500
@@ -5,7 +5,7 @@
 Meme-chip assumes the meme tools are in PATH.
 
 ========Tool data table conf========
-Add the entry from the sample to tool_data_table_conf.xml
+Check the entry is in tool_data_table_conf.xml
 
 ========Tool loc file========
 
--- a/meme_chip_wrapper.xml	Wed Nov 07 00:39:54 2012 -0500
+++ b/meme_chip_wrapper.xml	Mon Nov 12 18:09:08 2012 -0500
@@ -1,6 +1,6 @@
-<tool id="meme_chip_wrapper" name="meme-chip" version="1.0.0">
+<tool id="meme_chip_wrapper" name="meme-chip" version="1.2.1">
     <requirements>
-        <requirement type="package" version="4.9.0">meme-chip</requirement>
+        <requirement type="package" version="4.9.0">meme</requirement>
     </requirements>
     <description></description>
     <version_command>echo "MEME version r4.9.0"</version_command>
--- a/tool_data_table_conf.xml.sample	Wed Nov 07 00:39:54 2012 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Nov 12 18:09:08 2012 -0500
@@ -1,6 +1,8 @@
 <!-- Location of meme-chip files -->
+<tables>
       <table name="meme_chip_motifs" comment_char="#">
           <columns>value, name, path</columns>
           <file path="tool-data/meme_chip_motifs.loc" />
       </table>
+</tables>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Nov 12 18:09:08 2012 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="meme" version="4.9.0">
+    <install version="1.0">
+      <actions>
+        <!--<action type="download_by_url">ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/rc5/meme_4.9.0.tar.gz</action>-->
+        <action type="shell_command">touch $INSTALL_DIR/bin/dummyfile.sh</action>
+        <action type="shell_command">touch dummyfile.sh</action>
+        <action type="move_file">
+          <source>dummyfile.sh</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+      Skeleton file for meme install. Does not actually install meme.
+    </readme>
+  </package>
+</tool_dependency>