diff tool_dependencies.xml @ 0:8a8adbf98ecc draft

First upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri May 16 07:57:33 2014 -0400
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bowtie2" version="2.1.0">
+        <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="fastq_screen" version="0.4.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.4.2.tar.gz</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Galaxy wrapper for http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ from Simon Andrews.
+Useful if you want to (eg) check your RNA sequence from a cell culture for contamination from (eg) Mycoplasma Genitalium, or if you have sequence from an unknown organism :(
+Permanently set to use your Galaxy bowtie2 indices - expects Bowtie2 to be installed so the Galaxy package_bowtie2 is installed if it's not already there.
+
+###WARNING### The fastq_screen perl script requires that the GD::Graph http://search.cpan.org/~bwarfield/GDGraph/Graph.pm module be installed.
+Otherwise, NO plot will be created. This wrapper relies on the system perl - a proper Galaxy perl dependency is just too icky to think about.
+
+Send code if you think otherwise.
+        </readme>
+    </package>
+
+</tool_dependency>