Hi, I want to upload an imaging binary data file (*.ibd) which contains the mass spectral data (https://ms-imaging.org/wp/imzml/data-structure/) as input. So in my local instance, I need to add a new data type. The followings are my procedures:
galaxy/config/datatypes_conf.xml, I add
<datatype extension="ibd" type="galaxy.datatypes.binary:ibd" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />and
<sniffer type="galaxy.datatypes.binary:ibd" />
galaxy/lib/galaxy/datatypes/binary.py, I add
class ibd(_Binary ): """ Class describing an ibd file """ file_ext = "ibd" Binary.register_sniffable_binary_format("ibd", "ibd", ibd)
galaxy/lib/galaxy/datatypes/registry.py, add two lines:
'ibd' : binary.ibd(),and
'ibd' : 'application/octet-stream',
After uploading my ibd file, the data input box shows:
No ibd dataset avaible. And also History Pane indicated that the uploaded ibd file is empty with txt format. All of these indicate that the data type
ibd is not successfully added. Could someone help me to sort out this problem?
just double checking: - Have you restarted your galaxy server? - can you manually set the format to ibd?
Dear Hans, yes. I have restarted many times. And I have set the format in my galaxy tool
<param name="ibd_file" type="data" format="ibd" label="ibd file" help="This ibd file must be paired with imzML file. Make sure that selected ibd file must have the same file name of selected imzML above." />
...but can you manually set the format to ibd for a existing history item or using the upload tool?
"class ibd(_Binary ): " is the "_" a typo in your mail?
what happens if you remove the " subclass="true" "
Many thanks for your reply. Yes indeed it's a typo. After changing that, I can add the new data type. Unfortunately the uploaded binary data set is empty indicated by the History pane.