diff tools/mira4/README.rst @ 7:902f01c1084b draft

Uploaded v0.0.1 preview 7, with mirabait wrapper

--- a/tools/mira4/README.rst	Mon Oct 21 12:01:47 2013 -0400
+++ b/tools/mira4/README.rst	Fri Oct 25 07:18:38 2013 -0400
@@ -54,7 +54,9 @@
   <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 RC4. See:
+You will also need to install MIRA, we used version 4.0 RC4, and define the
+environment variable $MIRA4 pointing at the folder containing the binaries.
+See:
 
 * http://chevreux.org/projects_mira.html
 * http://sourceforge.net/projects/mira-assembler/
@@ -82,7 +84,7 @@
 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/mira4_validator.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
+    $ 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/mira4_validator.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 test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq
 
 Check this worked::
 
@@ -97,6 +99,11 @@
     test-data/tvc_contigs.fasta
     test-data/tvc_map_ref_strain.fasta
     test-data/tvc_map_same_strain.fasta
+    test-data/tvc_bait.fasta
+    test-data/tvc_mini_bait_pos.fastq
+    test-data/tvc_mini_bait_strict.fastq
+    test-data/tvc_mini_bait_neg.fastq
+
 
 
 Licence (MIT)