Hey Siemen, A workaround i'm currently using consists of creating an Xls subclass of the Binary datatype class:
In *galaxy-dist/lib/galaxy/datatypes/binary.py* add xls to * unsniffable_binary_formats* like this: *unsniffable_binary_formats = [ 'ab1', 'scf' , 'xls' ]* Also add the following class at the very end of the binary.py file: *class Xls(Binary):* * '''Class describing an Excel (xls) file'''* * * * file_ext = 'xls'* Then in your 'datatypes_conf.xml' add the following line (don't forget to comment out or remove other xls datatype lines): *<datatype extension="xls" type="galaxy.datatypes.binary:Xls" display_in_upload="true"/>* Then restart galaxy and when you upload an excel file you must explicitly select 'xls' for the 'File Format' (I personally don't know how to get 'Auto-detect' to work for added datatypes such as xls). If you have any questions about this implementation let me know. Good luck. Joe Cruz On Thu, Dec 8, 2011 at 3:11 AM, Siemen Sikkema <s.h.sikk...@gmail.com>wrote: > Hello! > > For our future galaxy users in Netherlands Bioinformatics Centre we'd like > to support Excel uploads. We have our own excel to tabular CLI tool and I > have been trying to get it working with galaxy. The tool itself is not the > problem, but getting excel files uploaded is… > > We're running a local instance (hg identify: 949e4f5fa03a+ tip) on Mac for > development purposes. > > The issues with excel are two-fold: XLSX files get unzipped automatically > and a useless XML file remains, while uploading an XLS file results in: > "The uploaded binary file contains inappropriate content". I've tried adding > > <datatype extension="xls" type="galaxy.datatypes.binary:Binary" > display_in_upload="true"/> > <datatype extension="xlsx" type="galaxy.datatypes.binary:Binary" > display_in_upload="true"/> > > to datatypes_conf.xml and selecting XLS and XLSX as datatype during upload > but to no avail (the errors don't change). > > A temporary workaround we thought of was to first zip the files before > uploading, that way Galaxy would unzip them and we'd be left with the raw > excel files. At first this seemed to work but the conversion did not. > Furthermore, downloading the files and trying to open them failed. A quick > 'diff' between the original and mangled files show differences practically > throughout the whole file! > > Now, my questions are as follows. Has work been underway to support excel > natively? Is there a way to have Galaxy simply accept uploaded files > without any interpretation? What happens inside Galaxy that corrupts the > excel files during unpacking? > > Thank you very much and I apologize if I somehow missed something obvious > or if these questions have been asked before. > > Kind regards, > Siemen Sikkema > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
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