Thanks. Is there a script that will delete all files older than a certain date
even if not marked as deleted by the user?
Thanks
Neil
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Thursday, July 17, 2014 5:42 PM
To: Burdett, Neil (DPS, Herston - RBWH);
On 07/17/2014 12:38 PM, neil.burd...@csiro.au wrote:
Thanks. Is there a script that will delete all files older than a certain date
even if not marked as deleted by the user?
I am not aware of such a script
Hans-Rudolf
Thanks
Neil
From:
Hi Greg,
not in the current, in version 2014-05-14, but I think the bug is
still there.
current version :
83for action_tup in filtered_actions:
84current_dir = os.path.abspath( os.path.join(
work_dir, dir ) )
Fix:
83for
Hello Peter,
Thanks for your answer.
I tried your come but I am still not able to make it work the way I want.
I mean that in the workflow design page, when I switch the parameter, it
doesn't change the graphical list of outputs of the tool. How can I fix it?
I want something like the Input,
On Thu, Jul 17, 2014 at 1:58 PM, Calogero Zarbo za...@fbk.eu wrote:
Hello Peter,
Thanks for your answer.
I tried your come but I am still not able to make it work the way I want.
I mean that in the workflow design page, when I switch the parameter, it
doesn't change the graphical list of
Ok, thanks for the the tip.
I changed the XML to this one:
outputs
data format=showelab-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
change_format
when input=format_options value=fbk
format=fbk-svm-dataset/
Hi John,
Thank you very much for your reply.
# I just want to clarify - do you have a tool with a multiple input data
# parameter (e.g. param type=data multiple=true ... ) as some
# intermediate step in a workflow? Or are you using a repeat or
# something?
I have a tool with a multiple input
On Thu, Jul 17, 2014 at 2:43 PM, Calogero Zarbo za...@fbk.eu wrote:
Ok, thanks for the the tip.
I changed the XML to this one:
outputs
data format=showelab-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
change_format
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For those reading this thread from the future, there's a secret to
adding completely new datatypes locally (and not through a toolshed).
You have to manually edit lib/galaxy/datatypes/registry.py and import
the module you've written at the top of the
Even more out of office than normal so maybe I don't have the throughput to
process this but it sounds like it won't work then. If the new types aren't
going to be loaded than we cannot evolve the datatypes with new
functionality in new repositories.
Perhaps I am missing something, but in the
Hi,
I think you are right John. Datatypes have many issues in that regard as
I can tell, from a few bug reports. Imho datatypes should be handled
like Tool dependency definitions. There should be only one
installable revsion.
But that aside, emboss datatypes are already broken. For example
On Thu, Jul 17, 2014 at 4:31 PM, Eric Rasche rasche.e...@yandex.ru wrote:
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For those reading this thread from the future, there's a secret to
adding completely new datatypes locally (and not through a toolshed).
You have to manually edit
On Thu, Jul 17, 2014 at 5:45 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi,
I think you are right John. Datatypes have many issues in that regard as I
can tell, from a few bug reports. Imho datatypes should be handled like
Tool dependency definitions. There should be only one
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Not a problem Peter, it's a somewhat subtle bug to have, and there isn't
a lot of documentation on the wiki about writing new datatypes (though I
plan to fix that soon).
That particular error message could stand to be a bit more explicit.
(e.g., Did
On Thu, Jul 17, 2014 at 5:55 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Not a problem Peter, it's a somewhat subtle bug to have, and there isn't
a lot of documentation on the wiki about writing new datatypes (though I
plan to fix that soon).
That particular error message could stand to be
Am 17.07.2014 18:51, schrieb Peter Cock:
On Thu, Jul 17, 2014 at 5:45 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi,
I think you are right John. Datatypes have many issues in that regard as I
can tell, from a few bug reports. Imho datatypes should be handled like
Tool dependency
Hi Dev Team,
I am attempting to get a new/clean installation running and am having
difficulty. I did a clone from https://bitbucket.org/galaxy/galaxy-dist and
made my needed configuration changes for my environment. I attempted to start
it and needed to do the database upgrade via sh
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On 07/17/2014 12:10 PM, Björn Grüning wrote:
Am 17.07.2014 18:51, schrieb Peter Cock:
On Thu, Jul 17, 2014 at 5:45 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi,
I think you are right John. Datatypes have many issues in that regard
On Thu, Jul 17, 2014 at 6:10 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
... but the problem will stay the same ... one [datatype definition]
repository
can have multiple versions ...
I like your idea that like tool dependency definitions, this should be a special
repository type on
On Thu, Jul 17, 2014 at 6:28 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Am 17.07.2014 18:51, schrieb Peter Cock:
One reason I have been meaning to do some of these is familiarity with
many of these formats from looking after/writing parsers in Biopython.
Peter, similar case here with
This would be easy to implement, but could adversely affect reproducibility.
If a repository containing datatypes always had only a single installable
revision (i.e., the chagelog tip), then any datatypes defined in an early
changeset revision that are removed in a later changeset revision
Good point Greg.
Let's refine this slightly then, a new special ToolShed repository type for
a *single* datatype definition. That avoids this problem :)
(This does not help with suites of very closely related datatypes -
like different
kinds of BLAST database.)
Peter
On Thu, Jul 17, 2014 at
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On 07/17/2014 12:31 PM, Peter Cock wrote:
On Thu, Jul 17, 2014 at 6:28 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Am 17.07.2014 18:51, schrieb Peter Cock:
One reason I have been meaning to do some of these is familiarity with
many of these
Here's a Trello card for this:
https://trello.com/c/s8tfbW4x
On Jul 17, 2014, at 1:38 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Good point Greg.
Let's refine this slightly then, a new special ToolShed repository type for
a *single* datatype definition. That avoids this problem :)
Hi all,
TLDR - Last 2 lines of this email
Some time ago we created a wrapper script for breseq, a tool that
generates a friendly HTML report of mutations.
This was a perfect match for Galaxy given that we could simply set the
summary.html file to be displayed using Galaxy's HTML datatype and
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Thanks to everyone for their assistance in my adventure of custom local
datatypes. In response to this, I've added a new wiki page with a basic
MWE/tutorial on adding datatypes. A complete example is at the end,
because most people like copy+paste
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Let's pretend for a second that I'm rather lazy (oh...wait), and I have
ZERO interest in writing datatype parsers to sniff and validate whether
or not a specific file is a specific datatype. I'm a sysadmin and
bioinformatician, and I've worked with
On 17 July 2014 22:29, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Jul 17, 2014 at 5:55 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Not a problem Peter, it's a somewhat subtle bug to have, and there isn't
a lot of documentation on the wiki about writing new datatypes (though I
plan
On Thu, Jul 17, 2014 at 7:19 PM, Eric Rasche rasche.e...@yandex.ru wrote:
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Thanks to everyone for their assistance in my adventure of custom local
datatypes. In response to this, I've added a new wiki page with a basic
MWE/tutorial on adding
You could do something like that, and we already have
Biopython packages in the ToolShed which can be listed
as dependencies :)
However, some things like GenBank are tricky - in order
to tolerate NCBI dumps the Biopython parser will ignore
any free text before the first LOCUS line. A confusing
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On 07/17/2014 02:11 PM, Peter Cock wrote:
You could do something like that, and we already have
Biopython packages in the ToolShed which can be listed
as dependencies :)
If my module depends on the biopython from the toolshed, will that be
On Thu, Jul 17, 2014 at 8:20 PM, Eric Rasche rasche.e...@yandex.ru wrote:
On 07/17/2014 02:11 PM, Peter Cock wrote:
You could do something like that, and we already have
Biopython packages in the ToolShed which can be listed
as dependencies :)
If my module depends on the biopython from the
How does the main Galaxy server deal with it? Users data can't remain on the
project's free server forever can it? and if not then there must be some
automated way of deleting data? is that correct?
Thanks
Neil
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent:
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Neil,
It'd be pretty easy to fix that yourself. In
scripts/cleanup_datasets/cleanup_datasets.py, there's a filter which
selects which datasets should be removed.
Check L350 of that script. You could simply remove the other values from
the _and
user
usernameemilybeck
quota_percent 19
total_disk_usage52086193970
nice_total_disk_usage 48.5 GB
email emily-b...@uiowa.edu
is_adminfalse
tags_used
model_class User
id 03f0554e2314759e
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Hello,
I have repeatedly gotten the following error message when attempting to use
both the mapping and pileup functions in Galaxy. I am using files that I have
previously used successfully with these functions, and cannot fix it.
Thank you.
~Emily Beck
user
usernameemilybeck
Thanks, but this doesn't work. As there are further checks in _purge_datasets
which check if the data has been deleted first. Can you purge data without
deleting it? If so I can remove those checks. Has anyone else needed to do this?
Thanks
neil
-Original Message-
From: Eric Rasche
Hi Hans,
Thank you for your advice. Thanks to other advice received from Iyad, I
was able to work out that my virtual python environment wasn¹t functioning
correctly. After I reinstalled it I managed to get going on the update.
However, I will keep this email on hand for future updates!
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