|
0
|
1 README
|
|
|
2 -----------------------------------------------------------------------
|
|
|
3 XCMS Suite datatypes: A Workflow for metabolomics by ABIMS team
|
|
|
4 -----------------------------------------------------------------------
|
|
|
5
|
|
|
6 This package contains the datatypes for the XCMS suite.
|
|
|
7
|
|
|
8 --------------------------------------------------------------------
|
|
|
9 Instructions for integration of the XCMS datatypes into the workflow-system
|
|
|
10 Galaxy (http://getgalaxy.org)
|
|
|
11 --------------------------------------------------------------------
|
|
|
12
|
|
|
13 In order to install the datatypes for the XCMS Suite into your Galaxy installation, please do the following:
|
|
|
14
|
|
|
15 $galaxybase: Your galaxy-dist location
|
|
|
16
|
|
|
17 -- Add the two datatypes and sniffer to the $galaxybase/datatypes_conf.xml
|
|
|
18
|
|
|
19 <datatype extension="ms_zip" type="galaxy.datatypes.xcms:MSZip" display_in_upload="true" />
|
|
|
20 <datatype extension="rdata" type="galaxy.datatypes.xcms:RData" display_in_upload="true" />
|
|
|
21 <sniffer type="galaxy.datatypes.xcms:MSZip"/>
|
|
|
22
|
|
|
23 -- Copy xcms.py to $galaxybase/lib/galaxy/datatypes/
|
|
|
24
|
|
|
25 -- Add "import xcms" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
|
|
|
26
|
|
|
27 -- Modify the $galaxybase/tools/data_source/upload.py:
|
|
|
28
|
|
|
29
|
|
|
30 -At the beginning of the file, put this line :
|
|
|
31 from galaxy.datatypes.xcms import *
|
|
|
32 -Then add the function:
|
|
|
33 def check_ms_zip( file_name ):
|
|
|
34 return MSZip().sniff( file_name )
|
|
|
35 -Add the following lines between the two <ABIMS insert lines> :
|
|
|
36
|
|
|
37 if image:
|
|
|
38 if not PIL:
|
|
|
39 image = None
|
|
|
40 # get_image_ext() returns None if nor a supported Image type
|
|
|
41 ext = get_image_ext( dataset.path, image )
|
|
|
42 data_type = ext
|
|
|
43 # Is dataset content multi-byte?
|
|
|
44 elif dataset.is_multi_byte:
|
|
|
45 data_type = 'multi-byte char'
|
|
|
46 ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
|
|
|
47 # <Abims insert Lines>
|
|
|
48 # Is dataset content supported Abims datatype
|
|
|
49 elif check_ms_zip( dataset.name ):
|
|
|
50 ext = 'ms_zip'
|
|
|
51 data_type = 'ms_zip'
|
|
|
52 # </Abims insert lines >
|
|
|
53 # Is dataset content supported sniffable binary?
|
|
|
54
|
|
|
55
|
|
|
56
|
|
|
57 Last but not least, restart Galaxy.
|
