Get Data and 'xlsx'
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions?
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML... It may also be useful to see your Galaxy data types configuration file. Peter On Wed, 10 Oct 2018 at 01:39, D K <danielfortin86@gmail.com> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions? ___________________________________________________________ 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: https://lists.galaxyproject.org/
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Sure, I've attached a sample xlsx file and my datatypes_conf.xml file Thanks! On Tue, Oct 9, 2018 at 11:52 PM Peter Cock <p.j.a.cock@googlemail.com> wrote:
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...
It may also be useful to see your Galaxy data types configuration file.
Peter
On Wed, 10 Oct 2018 at 01:39, D K <danielfortin86@gmail.com> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions? ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Hi all, I can confirm this file is sniffed as `format: blastxml` on usegalaxy.org, which is surely wrong. I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/6849 M. On Wed, Oct 10, 2018 at 2:11 PM D K <danielfortin86@gmail.com> wrote:
Sure, I've attached a sample xlsx file and my datatypes_conf.xml file
Thanks!
On Tue, Oct 9, 2018 at 11:52 PM Peter Cock <p.j.a.cock@googlemail.com> wrote:
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...
It may also be useful to see your Galaxy data types configuration file.
Peter
On Wed, 10 Oct 2018 at 01:39, D K <danielfortin86@gmail.com> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions? ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Thanks Martin, and D K, I've commented on https://github.com/galaxyproject/galaxy/issues/6849 but am puzzled as to what might be going on here. The BLAST XML sniffer code (which I wrote) is deliberately very selective with the intent of avoid any false positives. I would try it locally (thank you for sharing the test file), but right now it looks like a recent cluster change has disrupted our local Galaxy instance. Peter On Wed, Oct 10, 2018 at 7:20 PM Martin Čech <marten@bx.psu.edu> wrote:
Hi all,
I can confirm this file is sniffed as `format: blastxml` on usegalaxy.org, which is surely wrong.
I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/6849
M.
On Wed, Oct 10, 2018 at 2:11 PM D K <danielfortin86@gmail.com> wrote:
Sure, I've attached a sample xlsx file and my datatypes_conf.xml file
Thanks!
On Tue, Oct 9, 2018 at 11:52 PM Peter Cock <p.j.a.cock@googlemail.com> wrote:
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...
It may also be useful to see your Galaxy data types configuration file.
Peter
On Wed, 10 Oct 2018 at 01:39, D K <danielfortin86@gmail.com> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions? ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
participants (3)
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D K -
Martin Čech -
Peter Cock