# HG changeset patch
# User peterjc
# Date 1400669766 14400
# Node ID 8487d70e82aaf0b73c0bb99b16fb6c8ff558dd32
# Parent 381aa262c8cbe926ea2006cf3ff778b3da3f7b12
Uploaded v0.0.3 preview 1, target MIRA v4.0.2
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/README.rst
--- a/tools/mira4/README.rst Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/README.rst Wed May 21 06:56:06 2014 -0400
@@ -22,7 +22,7 @@
This should be straightforward. Via the Tool Shed, Galaxy should automatically
install the 'mira' datatype, samtools, and download and install the precompiled
-binary for MIRA v4.0 for the Galaxy wrapper, and run any tests.
+binary for MIRA v4.0.2 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).
@@ -56,7 +56,7 @@
-You will also need to install MIRA, we used version 4.0, and define the
+You will also need to install MIRA, we used version 4.0.2, and define the
environment variable ``$MIRA4`` pointing at the folder containing the binaries.
See:
@@ -85,11 +85,12 @@
------- ----------------------------------------------------------------------
v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
v0.0.2 - Include BAM output (using ``miraconvert`` and ``samtools``).
- - Updated to target MIRA 4.0
+ - Updated to target MIRA 4.0.1
- Simplified XML to apply input format to output data.
- Sets temporary folder at run time to respect environment variables
(``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
previously hard coded as ``/tmp``.
+v0.0.3 - Updated to target MIRA 4.0.2
======= ======================================================================
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4.py
--- a/tools/mira4/mira4.py Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4.py Wed May 21 06:56:06 2014 -0400
@@ -91,9 +91,12 @@
#but could be followed by a space in future...
text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())
+ #Want to try to ensure this gets written to disk before MIRA attempts
+ #to open it - any networked file system may impose a delay...
handle = open(manifest, "w")
handle.write(text)
handle.flush()
+ os.fsync(handle.fileno())
handle.close()
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4_bait.xml
--- a/tools/mira4/mira4_bait.xml Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4_bait.xml Wed May 21 06:56:06 2014 -0400
@@ -1,4 +1,4 @@
-
+
Filter reads using kmer matches
mirabait
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4_de_novo.xml
--- a/tools/mira4/mira4_de_novo.xml Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4_de_novo.xml Wed May 21 06:56:06 2014 -0400
@@ -1,4 +1,4 @@
-
+
Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads
mira
@@ -82,7 +82,7 @@
project = MIRA
job = denovo,${job_type},${job_quality}
-parameters = -NW:cmrnl=no -DI:trt=/tmp
+parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no
## -GE:not is short for -GENERAL:number_of_threads and using one (1)
## can be useful for repeatability of assemblies and bug hunting.
## This is overriden by the command line -t switch which is easier
@@ -95,6 +95,9 @@
## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
## point to a local hard drive (not something like NFS on network).
## We replace /tmp with an environment variable via mira4.py
+##
+## -OUT:orc=no is short for -OUTPUT:output_result_caf=no
+## which turns off an output file we don't want anyway.
#for $rg in $read_group
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4_mapping.xml
--- a/tools/mira4/mira4_mapping.xml Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4_mapping.xml Wed May 21 06:56:06 2014 -0400
@@ -1,4 +1,4 @@
-
+
Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads
mira
@@ -80,7 +80,7 @@
project = MIRA
job = mapping,${job_type},${job_quality}
-parameters = -NW:cmrnl=no -DI:trt=/tmp
+parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no
## -GE:not is short for -GENERAL:number_of_threads and using one (1)
## can be useful for repeatability of assemblies and bug hunting.
## This is overriden by the command line -t switch which is easier
@@ -93,6 +93,9 @@
## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
## point to a local hard drive (not something like NFS on network).
## We replace /tmp with an environment variable via mira4.py
+##
+## -OUT:orc=no is short for -OUTPUT:output_result_caf=no
+## which turns off an output file we don't want anyway.
##This bar goes into the manifest as a comment line
#------------------------------------------------------------------------------
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/tool_dependencies.xml
--- a/tools/mira4/tool_dependencies.xml Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/tool_dependencies.xml Wed May 21 06:56:06 2014 -0400
@@ -1,14 +1,14 @@
-
+
- http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_darwin13.0.0_x86_64_static.tar.bz2
+ http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2
bin
$INSTALL_DIR
@@ -16,7 +16,7 @@
- https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2
+ http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2
bin
$INSTALL_DIR
@@ -43,7 +43,7 @@
-Downloads MIRA v4.0 from Sourceforge, requesting Bastien's precompiled binaries
+Downloads MIRA v4.0.2 from Sourceforge, requesting Bastien's precompiled binaries
for 64 bit (x86_64) Linux or Mac OS X. Other platforms where compilation from
source would be required (e.g. 32 bit Linux) are not supported by this automated
installation script.