Mercurial > repos > peterjc > mira4_assembler

changeset 12:a6a56440567c draft

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Uploaded v0.0.2 preview 4, now using MIRA 4.0 (not RC), and sets MIRA4 environment variable during install.
author peterjc
date Mon, 03 Feb 2014 06:25:35 -0500
parents 02350bef2e99
children 7fcabeeca5df
files tools/mira4/README.rst tools/mira4/mira4.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml
diffstat 4 files changed, 12 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/tools/mira4/README.rst	Tue Dec 10 06:29:13 2013 -0500
+++ b/tools/mira4/README.rst	Mon Feb 03 06:25:35 2014 -0500
@@ -56,7 +56,7 @@
   <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 RC5, and define the
+You will also need to install MIRA, we used version 4.0, and define the
 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
 See:
 
@@ -85,7 +85,7 @@
 ------- ----------------------------------------------------------------------
 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 RC5
+        - Updated to target MIRA 4.0
 ======= ======================================================================
 
 
--- a/tools/mira4/mira4.py	Tue Dec 10 06:29:13 2013 -0500
+++ b/tools/mira4/mira4.py	Mon Feb 03 06:25:35 2014 -0500
@@ -36,7 +36,7 @@
 
 try:
     mira_path = os.environ["MIRA4"]
-except ImportError:
+except KeyError:
     stop_err("Environment variable $MIRA4 not set")
 mira_binary = os.path.join(mira_path, "mira")
 if not os.path.isfile(mira_binary):
--- a/tools/mira4/mira4_bait.py	Tue Dec 10 06:29:13 2013 -0500
+++ b/tools/mira4/mira4_bait.py	Mon Feb 03 06:25:35 2014 -0500
@@ -39,7 +39,7 @@
 
 try:
     mira_path = os.environ["MIRA4"]
-except ImportError:
+except KeyError:
     stop_err("Environment variable $MIRA4 not set")
 mira_binary = os.path.join(mira_path, "mirabait")
 if not os.path.isfile(mira_binary):
--- a/tools/mira4/tool_dependencies.xml	Tue Dec 10 06:29:13 2013 -0500
+++ b/tools/mira4/tool_dependencies.xml	Mon Feb 03 06:25:35 2014 -0500
@@ -8,7 +8,7 @@
             <actions_group>
                 <!-- Download the binaries for MIRA compatible with 64-bit OSX. -->
                 <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc5_darwin13.0.0_x86_64_static.tar.bz2</action>
+                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_darwin13.0.0_x86_64_static.tar.bz2</action>
                     <action type="move_directory_files">
                          <source_directory>bin</source_directory>
                          <destination_directory>$INSTALL_DIR</destination_directory>
@@ -16,7 +16,7 @@
                 </actions>
                 <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc5_linux-gnu_x86_64_static.tar.bz2</action>
+                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>bin</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
@@ -37,13 +37,16 @@
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                 </action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="MIRA4">$INSTALL_DIR</environment_variable>
+                </action>
             </actions_group>
         </install>
         <readme>
 Downloads MIRA v4.0 from Sourceforge, requesting Bastien's precompiled binaries
-for 64 bit (x86_64) Linux or Mac OS X. Other platforms were compilation from
-source would be required (e.g. 32 bit Linux and Mac) are not supported by this
-automated installation script.
+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.
 
 http://chevreux.org/projects_mira.html
 http://sourceforge.net/projects/mira-assembler/