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author | mish |
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date | Wed, 23 Apr 2014 05:25:23 -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.