Mercurial > repos > nikos > hrf_seq

diff tool_dependencies.xml @ 2:14d6929f8aa1 draft default tip

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Tool tests or/and test-data are missing.
author nikos
date Thu, 11 Sep 2014 08:30:05 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 11 08:30:05 2014 -0400
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="cutadapt" version="1.4.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://pypi.python.org/packages/source/c/cutadapt/cutadapt-1.4.2.tar.gz</action>
+                <action type="shell_command">python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+    <package name="bowtie2" version="2.1.0">
+        <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.18">
+	<repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>