diff tools/mira4/README.rst @ 4:df86ed992a1b draft

Uploaded preview 4, lots of work on mapping

--- a/tools/mira4/README.rst	Thu Sep 26 12:30:08 2013 -0400
+++ b/tools/mira4/README.rst	Fri Oct 11 04:28:45 2013 -0400
@@ -37,7 +37,7 @@
 
 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes 
 
-There are just two Galaxy files to install:
+There are just three Galaxy files to install:
 
 * mira4.py (the Python script)
 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
@@ -50,7 +50,7 @@
   <tool file="mira4/mira4_de_novo.xml" />
   <tool file="mira4/mira4_mapping.xml" />
 
-You will also need to install MIRA, we used version 4.0 RC2. See:
+You will also need to install MIRA, we used version 4.0 RC3. See:
 
 * http://chevreux.org/projects_mira.html
 * http://sourceforge.net/projects/mira-assembler/
@@ -65,7 +65,7 @@
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
-v0.0.1  - Initial version (prototype using MIRA 4.0 RC2, and wrapper for v3.4)
+v0.0.1  - Initial version (prototype for MIRA 4.0 RC3, based on wrapper for v3.4)
 ======= ======================================================================
 
 
@@ -73,12 +73,12 @@
 ==========
 
 Development is on a dedicated GitHub repository:
-https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0
+https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
 
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder::
 
-    $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs_mira4.fasta
+    $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta
 
 Check this worked::
 
@@ -89,7 +89,9 @@
     tools/mira4/mira4.py
     tools/mira4/tool_dependencies.xml
     test-data/tvc_mini.fastq
-    test-data/tvc_contigs_mira4.fasta
+    test-data/tvc_contigs.fasta
+    test-data/tvc_map_ref_strain.fasta
+    test-data/tvc_map_same_strain.fasta
 
 
 Licence (MIT)