diff cgatools/README.txt @ 20:382c50ce0519 draft

Uploaded

--- a/cgatools/README.txt	Fri Jun 22 15:49:43 2012 -0400
+++ b/cgatools/README.txt	Tue Sep 04 18:46:40 2012 -0400
@@ -1,11 +1,15 @@
 Provides galaxy tools for Complete Genomics' cgatools package -  http://www.completegenomics.com
 
 This repository provides tools to execute functions of cgatools from Complete Genomics, Inc. 
-and includes the cgatools 1.5 executable.
+and includes the cgatools 1.6 executable.
  
-Reference genomes files for cgatools can be downloaded from Complete Genomics ftp site:
+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
+
+Calibration files for cgatools can be downloaded from Complete Genomics' ftp site:
+ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz
+
 After copying the files in the desired locations follow the instructions below to register
 the reference files with galaxy.
 
@@ -15,7 +19,7 @@
 AUTOMATIC INSTALL
 
 When prompted for a tool panel section to contain the installed tools create a new section 
-called 'Complete Genomics - cgatools 1.5'.
+called 'Complete Genomics - cgatools 1.6'.
 
 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 
@@ -29,7 +33,7 @@
 MANUAL INSTALL
 
 For manual install from compressed files move/copy the following files into your Galaxy instance:
-directory tools/cgatools_v1.5                       to   tools/
+directory tools/cgatools_1.6                        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
 
@@ -38,17 +42,20 @@
 
 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
+    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 name="Complete Genomics - cgatools 1.6" id="cg_cgatools1.6">
+    <tool file="cgatools_1.6/listvariants.xml" />
+    <tool file="cgatools_1.6/testvariants.xml" />
+    <tool file="cgatools_1.6/listtestvariants.xml" />
+    <tool file="cgatools_1.6/calldiff.xml" />
+    <tool file="cgatools_1.6/snpdiff.xml" />
+    <tool file="cgatools_1.6/junctiondiff.xml" />
+    <tool file="cgatools_1.6/join.xml" />
+    <tool file="cgatools_1.6/varfilter.xml" />
+    <tool file="cgatools_1.6/mkvcf.xml" />
+    <tool file="cgatools_1.6/evidence2sam.xml" />
   </section>
   <!-- End of copied section -->