Mercurial > repos > jjohnson > package_bowtie_2_1_0

changeset 0:38652b57e057 draft default tip

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author jjohnson
date Tue, 20 Aug 2013 11:16:25 -0400
parents
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files tool_dependencies.xml
diffstat 1 files changed, 37 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Aug 20 11:16:25 2013 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bowtie" version="2.1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
+                <action type="shell_command">make BITS=64</action>
+                <action type="move_file">
+                    <source>bowtie2</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-build</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-align</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-inspect</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Program: bowtie2 (ultrafast, memory-efficient short read aligner)
+Version: 2.1.0 
+http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+
+Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
+        </readme>
+    </package>
+</tool_dependency>