Mercurial > repos > lomereiter > sambamba_filter

changeset 5:123168c85390

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updated to 0.4.7; use precompiled binaries
author lomereiter <lomereiter@gmail.com>
date Tue, 04 Nov 2014 18:34:37 +0300
parents 6d875183e6f7
children f81259dcaea7
files sambamba_filter.xml tool_dependencies.xml
diffstat 2 files changed, 33 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/sambamba_filter.xml	Wed Jul 24 13:33:50 2013 -0400
+++ b/sambamba_filter.xml	Tue Nov 04 18:34:37 2014 +0300
@@ -1,6 +1,6 @@
-<tool id="sambamba_filter" name="Filter BAM or SAM" version="1.0">
+<tool id="sambamba_filter" name="Filter BAM or SAM" version="1.1">
     <requirements>
-        <requirement type="package" version="0.3.3">sambamba</requirement>
+        <requirement type="package" version="0.4.7">sambamba</requirement>
     </requirements>
     <description>
         on flags, fields, and tags using Sambamba
@@ -20,7 +20,7 @@
         #set $input1 = 'input.bam'
         ln -s $input $input1 &amp;&amp;
         ln -s $input.metadata.bam_index input.bai &amp;&amp;
-        sambamba view 
+        sambamba view -t \${GALAXY_SLOTS:-8}
         #if $query != "":
             --filter="$query"
         #end if
@@ -71,8 +71,6 @@
 Filter Syntax 
 =============
 
-Complete documentation of filter syntax is available at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax.
-
 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.
 
 *Basic condition* is a one for a single record field, tag, or flag.
@@ -157,7 +155,6 @@
 -----
 
 .. _sambamba: http://github.com/lomereiter/sambamba
-.. _filter-syntax: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax
 
     </help>
 </tool>
--- a/tool_dependencies.xml	Wed Jul 24 13:33:50 2013 -0400
+++ b/tool_dependencies.xml	Tue Nov 04 18:34:37 2014 +0300
@@ -1,36 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="sambamba" version="0.3.3">
-        <install version="1.0">
-            <actions>
-				<action type="shell_command">git clone --recursive https://github.com/lomereiter/sambamba</action>
-                <action type="shell_command">git checkout v0.3.3</action>
-                <action type="shell_command">git submodule update --recursive</action>
-                <action type="shell_command">make release</action>
-                <action type="move_directory_files">
-                    <source_directory>build</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-		</install>
-		<readme>
- This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
-
-There are a three options for installation of sambamba:
-
-	1) Automated toolshed installation.  This requires that a D2 compiler (dmd >= 2.063) is installed.  The automated installation will attempt to use the dmd compiler and thus **will not be optimized**.  
-
-	2) Manual compilation.  For performance reasons, the sambamba developers recommend you use either GDC or LDC as they use GCC and LLVM backends and do a much better job at optimization.  You should then use the sambamba-ldmd2-64 make target.  See https://github.com/lomereiter/sambamba/wiki/Command-line-tools for more information.
-
-	3) Precompiled binary (recommended).  You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba.  
-
-If you choose option 2 or 3, sambamba may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir".  See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. 
-
-The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper.
-The sambamba development repository is at: https://github.com/lomereiter/sambamba.
-        </readme>
-    </package>
+  <package name="sambamba" version="0.4.7">
+    <install version="1.0">
+      <actions_group>
+        <actions os="darwin" architecture="x86_64">
+          <action type="download_by_url">
+            https://github.com/lomereiter/sambamba/releases/download/v0.4.7/sambamba_v0.4.7_osx.tar.bz2
+          </action>
+          <action type="move_file">
+            <source>sambamba_v0.4.7</source>
+            <destination>$INSTALL_DIR/bin/sambamba</destination>
+          </action>
+        </actions>
+        <actions os="linux" architecture="x86_64">
+          <action type="download_by_url">
+            https://github.com/lomereiter/sambamba/releases/download/v0.4.7/sambamba_v0.4.7_centos5.tar.bz2
+          </action>
+          <action type="move_file">
+            <source>sambamba_v0.4.7</source>
+            <destination>$INSTALL_DIR/bin/sambamba</destination>
+          </action>
+        </actions>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions_group>
+    </install>
+    <readme>
+      Downloads the precompiled 64bit Linux or Mac OS X binaries from the official repository 'Releases' section.
+    </readme>
+  </package>
 </tool_dependency>