diff cgatools/README.txt @ 17:6a5889dac45b draft

Uploaded

--- a/cgatools/README.txt	Thu Jun 14 13:51:46 2012 -0400
+++ b/cgatools/README.txt	Mon Jun 18 19:47:01 2012 -0400
@@ -1,3 +1,74 @@
 Provides galaxy tools for Complete Genomics' cgatools package -  http://www.completegenomics.com
 
-Create new section 'Complete Genomics' if it doesn't already exist in your tool panel.
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+This repository provides tools to execute functions of cgatools from Complete Genomics, Inc. 
+and includes the cgatools 1.5 executable.
+ 
+Reference genomes files for cgatools can be downloaded from Complete Genomics ftp site:
+ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
+ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
+After copying the files in the desired locations follow the instructions below to register
+the reference files with galaxy.
+
+
+
+
+AUTOMATIC INSTALL
+
+When prompted for a tool panel section to contain the installed tools create a new section 
+called 'Complete Genomics - cgatools 1.5'.
+
+After install create a cg_ccr_files.loc file in the tool-data directory of your Galaxy 
+instance by copying the cg_ccr_files.loc.sample file. In cg_ccr_files.loc edit the path 
+for the reference genome files (.crr files) downloaded from Complete Genomics' ftp site.
+
+Restart Galaxy instance after editing cg_crr_files.loc.
+
+
+
+
+MANUAL INSTALL
+
+For manual install from compressed files move/copy the following files into your Galaxy instance:
+directory tools/cgatools_v1.5                       to   tools/
+file      lib/galaxy/datatypes/completegenomics.py  to   lib/galaxy/datatypes/
+file      tool-data/cg_crr_files.loc.sample         to   tool-data/cg_crr_files.loc
+
+In cg_ccr_files.loc edit the path for the reference genome files (.crr files) downloaded 
+from Complete Genomics' ftp site.
+
+Paste from tool_config.xml.sample into the tool_config.xml of your Galaxy instance:
+  <!-- 
+    Copy the following section to tool_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
+  -->
+  <section name="Complete Genomics - cgatools v1.5" id="cg_cgatools1.5">
+    <tool file="cgatools_v1.5/listvariants.xml" />
+    <tool file="cgatools_v1.5/testvariants.xml" />
+    <tool file="cgatools_v1.5/listtestvariants.xml" />
+    <tool file="cgatools_v1.5/calldiff.xml" />
+    <tool file="cgatools_v1.5/snpdiff.xml" />
+    <tool file="cgatools_v1.5/junctiondiff.xml" />
+    <tool file="cgatools_v1.5/join.xml" />
+    <tool file="cgatools_v1.5/varfilter.xml" />
+  </section>
+  <!-- End of copied section -->
+
+Paste from tool_data_table_config.xml.sample into the tool_data_table_config.xml of your Galaxy instance:
+    <!-- Start location of cgatools crr files -->
+    <table name="cg_crr_files" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/cg_crr_files.loc" />
+    </table>
+    <!-- End Location of cgatools crr files -->
+
+Paste from datatypes_conf.xml into the datatypes_conf.xml of your Galaxy instance:
+    <!-- 
+      Copy the following section to datatypes_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
+    -->
+    <!-- Start Complete Genomics Datatypes -->
+    <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
+    <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
+    <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
+    <!-- End Complete Genomics Datatypes -->
+    <!-- End of copied section -->
+    
+Restart Galaxy instance.
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