diff tools/mira4/README.rst @ 9:302d13490b23 draft

Uploaded v0.0.2 preview 1, BAM output

--- a/tools/mira4/README.rst	Mon Oct 28 05:44:46 2013 -0400
+++ b/tools/mira4/README.rst	Thu Nov 28 05:07:59 2013 -0500
@@ -21,8 +21,8 @@
 ======================
 
 This should be straightforward. Via the Tool Shed, Galaxy should automatically
-install the 'mira' datatype, download and install the precompiled binary for
-MIRA v4.0 for the Galaxy wrapper, and run any tests.
+install the 'mira' datatype, samtools, and download and install the precompiled
+binary for MIRA v4.0 for the Galaxy wrapper, and run any tests.
 
 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
@@ -42,20 +42,22 @@
 
 There are four Galaxy files to install:
 
-* mira4.py (the Python wrapper script)
-* mira4_validator.py (the Python parameter validation script)
-* mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
-* mira4_mapping.xml (the Galaxy tool definition for mapping usage)
+* ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage)
+* ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
+* ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
+* ``mira4.py`` (the Python wrapper script)
+* ``mira_bait.py`` (the Python wrapper script for mirabait)
+* ``mira4_validator.py`` (the XML parameter validation script)
 
-The suggested location is a new tools/mira4 folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
-this to tools_conf.xml.sample in order to run any tests::
+The suggested location is a new ``tools/mira4`` folder. You will also need to
+modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
+this to ``tools_conf.xml.sample`` in order to run the tests::
 
   <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, and define the
-environment variable $MIRA4 pointing at the folder containing the binaries.
+environment variable ``$MIRA4`` pointing at the folder containing the binaries.
 See:
 
 * http://chevreux.org/projects_mira.html
@@ -64,6 +66,16 @@
 You may wish to use different cluster setups for the de novo and mapping
 tools, see above.
 
+You will also need to install samtools (for generating a BAM file from MIRA's
+SAM output).
+
+After copying (or symlinking) the ``test-data`` files under Galaxy's ``test-data``
+folder, you can run the tests with::
+
+    $ ./run_functional_tests.sh -id mira_4_0_bait
+    $ ./run_functional_tests.sh -id mira_4_0_de_novo
+    $ ./run_functional_tests.sh -id mira_4_0_mapping
+
 
 History
 =======
@@ -72,6 +84,7 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
+v0.0.2  - Include BAM output (using ``miraconvert`` and ``samtools``).
 ======= ======================================================================
 
 
@@ -84,7 +97,7 @@
 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 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
+    $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_bait.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::
 
@@ -92,8 +105,11 @@
     tools/mira4/README.rst
     tools/mira4/mira4_de_novo.xml
     tools/mira4/mira4_mapping.xml
+    tools/mira4/mira4_bait.xml
     tools/mira4/mira4.py
+    tools/mira4/mira4_make_bam.py
     tools/mira4/mira4_validator.py
+    tools/mira4/mira4_bait.py
     tools/mira4/tool_dependencies.xml
     test-data/tvc_mini.fastq
     test-data/tvc_contigs.fasta