Mercurial > repos > stheil > package_idba

changeset 0:1fde0b7d7d40 draft default tip

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author stheil
date Thu, 24 Sep 2015 11:57:36 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 137 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 24 11:57:36 2015 -0400
@@ -0,0 +1,137 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="idba" version="1.0">
+    <install version="1.0">
+      <actions>
+        <action type="shell_command">git clone https://github.com/loneknightpy/idba.git idba</action>
+        <action type="change_directory">idba</action>
+        <action type="shell_command">./build.sh</action>
+        <action type="shell_command">./configure</action>
+        <action type="shell_command">make</action>
+        <action type="move_file">
+          <source>bin/fa2fq</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/filter_blat</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/filter_contigs</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/filterfa</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/fq2fa</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/idba</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/idba_hybrid</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/idba_tran</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/idba_tran_test</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/idba_ud</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/parallel_blat</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/parallel_rna_blat</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/print_graph</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/raw_n50</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/sample_reads</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/scaffold</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/shuffle_reads</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/sim_reads</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/sim_reads_tran</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/sort_psl</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/sort_reads</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/split_fa</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/split_fq</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/split_scaffold</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/test</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/validate_component</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/validate_contigs_blat</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/validate_contigs_mummer</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/validate_reads_blat</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="move_file">
+          <source>bin/validate_rna</source>
+          <destination>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+  </package>
+</tool_dependency>