Mercurial > repos > mish > datatypes
diff xcms_datatypes/README.txt @ 0:d00379767dbf draft default tip
Uploaded
author | mish |
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date | Wed, 23 Apr 2014 05:25:23 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_datatypes/README.txt Wed Apr 23 05:25:23 2014 -0400 @@ -0,0 +1,57 @@ +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.