diff xcms_datatypes/README.txt @ 0:d00379767dbf draft default tip

Uploaded

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+++ b/xcms_datatypes/README.txt	Wed Apr 23 05:25:23 2014 -0400
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+README
+-----------------------------------------------------------------------
+   XCMS Suite datatypes: A Workflow for metabolomics by ABIMS team
+-----------------------------------------------------------------------
+
+This package contains the datatypes for the XCMS suite.
+
+--------------------------------------------------------------------
+Instructions for integration of the XCMS datatypes into the workflow-system
+Galaxy (http://getgalaxy.org)
+--------------------------------------------------------------------
+
+In order to install the datatypes for the XCMS Suite into your Galaxy installation, please do the following:
+
+$galaxybase: Your galaxy-dist location
+
+-- Add the two datatypes and sniffer to the $galaxybase/datatypes_conf.xml
+
+        <datatype extension="ms_zip" type="galaxy.datatypes.xcms:MSZip" display_in_upload="true" />
+		<datatype extension="rdata" type="galaxy.datatypes.xcms:RData" display_in_upload="true" />
+		<sniffer type="galaxy.datatypes.xcms:MSZip"/>
+
+-- Copy xcms.py to $galaxybase/lib/galaxy/datatypes/
+
+-- Add "import xcms" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
+
+-- Modify the $galaxybase/tools/data_source/upload.py:
+
+
+	-At the beginning of the file, put this line :
+		from galaxy.datatypes.xcms import *
+	-Then add the function:
+		def check_ms_zip( file_name ):
+		return MSZip().sniff( file_name )
+	-Add the following lines between the two <ABIMS insert lines> :
+	
+	if image:
+			if not PIL:
+				image = None
+			# get_image_ext() returns None if nor a supported Image type
+			ext = get_image_ext( dataset.path, image )
+			data_type = ext
+		# Is dataset content multi-byte?
+		elif dataset.is_multi_byte:
+			data_type = 'multi-byte char'
+		ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
+		# <Abims insert Lines>
+		# Is dataset content supported Abims datatype
+		elif check_ms_zip( dataset.name ):
+			ext = 'ms_zip'
+			data_type = 'ms_zip'
+		# </Abims insert lines >
+		# Is dataset content supported sniffable binary?
+
+
+
+Last but not least, restart Galaxy.