Mercurial > repos > kevyin > meme_chip

changeset 16:c3e0e0a0ae09 draft

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Uploaded
author kevyin
date Mon, 12 Nov 2012 19:34:55 -0500
parents a6a92a8fe166
children 5bb9eb050e57
files README meme_chip_wrapper.xml tool_dependencies.xml
diffstat 3 files changed, 19 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/README	Mon Nov 12 01:17:03 2012 -0500
+++ b/README	Mon Nov 12 19:34:55 2012 -0500
@@ -1,11 +1,19 @@
 Meme-chip wrapper for Galaxy
 
+=========================================:
 ========Installation instructions========:
-First make sure meme is installed and accessible from the command line.
+=========================================:
+The tool_dependencies.xml can attempt to install meme in a folder specific for this tool.
+(such as bwa_wrappers)
+
+The procedure does NOT download motif databases you will need to download them yourself
+
 Meme-chip assumes the meme tools are in PATH.
+Make sure meme is accessible
+
 
 ========Tool data table conf========
-Check the entry is in tool_data_table_conf.xml
+Check the meme_chip_motifs entry is in tool_data_table_conf.xml
 
 ========Tool loc file========
 
@@ -22,9 +30,11 @@
 After running delete the loc entries with multiple paths eg. All Vertebrates
 
 
+=========================================:
 LICENSE for this wrapper: 
+=========================================:
 Kevin Ying
-Garvan Institute http://www.garvan.org.au
-GVL https://genome.edu.au/wiki/GVL
+Garvan Institute: http://www.garvan.org.au
+GVL: https://genome.edu.au/wiki/GVL
 
 http://opensource.org/licenses/mit-license.php
--- a/meme_chip_wrapper.xml	Mon Nov 12 01:17:03 2012 -0500
+++ b/meme_chip_wrapper.xml	Mon Nov 12 19:34:55 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="meme_chip_wrapper" name="meme-chip" version="1.2.1">
+<tool id="meme_chip_wrapper" name="meme-chip" version="1.2.3">
     <requirements>
         <requirement type="package" version="4.9.0">meme</requirement>
     </requirements>
--- a/tool_dependencies.xml	Mon Nov 12 01:17:03 2012 -0500
+++ b/tool_dependencies.xml	Mon Nov 12 19:34:55 2012 -0500
@@ -3,12 +3,10 @@
   <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 dummyfile</action>
-        <action type="move_file">
-          <source>dummyfile</source>
-          <destination>$INSTALL_DIR/bin</destination>
-        </action>
+        <action type="download_by_url">ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/rc5/meme_4.9.0.tar.gz</action>
+        <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+        <action type="shell_command">make</action>
+        <action type="shell_command">make install</action>
         <action type="set_environment">
           <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
         </action>