9:18 p.m.
Hi All,
I'm looking to batch process 40 large data sets with the same galaxy
workflow.
This obviously can be done in a brute-force manual manner.
However, is there a better way to schedule/invoke these jobs in batch
1) from the UI with a plugin
2) command-line
3) web-service
Thanks in advance for any pointers.
Dave
9:27 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
Hi Dave,
Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple
datasets as input for a single "Input Dataset" step. To do this, click the icon
referenced by the tooltip in the screenshot below to select multiple files. All
parameters remain static between executions except for the single input dataset that gets
modified for each run, and that only one input dataset can be set to multiple files in
this fashion.
-Dannon
On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:
Hi All,
I'm looking to batch process 40 large data sets with the same galaxy workflow.
This obviously can be done in a brute-force manual manner.
However, is there a better way to schedule/invoke these jobs in batch
1) from the UI with a plugin
2) command-line
3) web-service
Thanks in advance for any pointers.
Dave
___________________________________________________________
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9:53 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
Thank you Dannon. That is helpful.
What if I need to specify multiple inputs per run (i.e. .csfasta + .qual
file)?
-Dave
On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker <dannonbaker(a)me.com> wrote:
Hi Dave,
Yes, galaxy's standard run-workflow dialog has a feature where you can
select multiple datasets as input for a single "Input Dataset" step. To do
this, click the icon referenced by the tooltip in the screenshot below to
select multiple files. All parameters remain static between executions
except for the single input dataset that gets modified for each run, and
that only one input dataset can be set to multiple files in this fashion.
-Dannon
On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:
Hi All,
I'm looking to batch process 40 large data sets with the same galaxy
workflow.
This obviously can be done in a brute-force manual manner.
However, is there a better way to schedule/invoke these jobs in batch
1) from the UI with a plugin
2) command-line
3) web-service
Thanks in advance for any pointers.
Dave
___________________________________________________________
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/
10 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
This method only works for single inputs at the moment, though eventually it'd be nice
to allow pairing. Another option for you would be to use the workflows API, with which
you can definitely specify multiple inputs. See workflow_execute.py in the scripts/api
folder of your galaxy installation for one method of doing this.
-Dannon
On Feb 6, 2012, at 4:53 PM, Dave Lin wrote:
Thank you Dannon. That is helpful.
What if I need to specify multiple inputs per run (i.e. .csfasta + .qual file)?
-Dave
On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker <dannonbaker(a)me.com> wrote:
Hi Dave,
Yes, galaxy's standard run-workflow dialog has a feature where you can select
multiple datasets as input for a single "Input Dataset" step. To do this, click
the icon referenced by the tooltip in the screenshot below to select multiple files. All
parameters remain static between executions except for the single input dataset that gets
modified for each run, and that only one input dataset can be set to multiple files in
this fashion.
-Dannon
<PastedGraphic-2.png>
On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:
> Hi All,
>
> I'm looking to batch process 40 large data sets with the same galaxy workflow.
>
> This obviously can be done in a brute-force manual manner.
>
> However, is there a better way to schedule/invoke these jobs in batch
>
> 1) from the UI with a plugin
> 2) command-line
> 3) web-service
>
> Thanks in advance for any pointers.
> Dave
>
> ___________________________________________________________
> 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/
1:03 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
Hello Dannon
Could it be possible to have the input dataset's display name appended
to the new history's name instead of plain numbers when the "Send
results in a new history" option is checked?
This new feature is indeed veeeeery useful (thanks a million for it) but
the numbered suffixes make it hard to track what new history belongs to
which dataset.
Thanks,
L-A
Le 06/02/2012 23:00, Dannon Baker a écrit :
This method only works for single inputs at the moment, though
eventually it'd be nice to allow pairing. Another option for you would be to use the
workflows API, with which you can definitely specify multiple inputs. See
workflow_execute.py in the scripts/api folder of your galaxy installation for one method
of doing this.
-Dannon
On Feb 6, 2012, at 4:53 PM, Dave Lin wrote:
> Thank you Dannon. That is helpful.
>
>
> What if I need to specify multiple inputs per run (i.e. .csfasta + .qual file)?
>
> -Dave
>
> On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker<dannonbaker(a)me.com> wrote:
> Hi Dave,
>
> Yes, galaxy's standard run-workflow dialog has a feature where you can select
multiple datasets as input for a single "Input Dataset" step. To do this, click
the icon referenced by the tooltip in the screenshot below to select multiple files. All
parameters remain static between executions except for the single input dataset that gets
modified for each run, and that only one input dataset can be set to multiple files in
this fashion.
>
> -Dannon
>
> <PastedGraphic-2.png>
>
>
>
>
>
> On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:
>
>> Hi All,
>>
>> I'm looking to batch process 40 large data sets with the same galaxy
workflow.
>>
>> This obviously can be done in a brute-force manual manner.
>>
>> However, is there a better way to schedule/invoke these jobs in batch
>>
>> 1) from the UI with a plugin
>> 2) command-line
>> 3) web-service
>>
>> Thanks in advance for any pointers.
>> Dave
>>
>> ___________________________________________________________
>> 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/
>
___________________________________________________________
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:
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1:25 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
Thanks for the suggestion, I like that! I'll make the change shortly.
-Dannon
On Feb 7, 2012, at 8:03 AM, Louise-Amélie Schmitt wrote:
Hello Dannon
Could it be possible to have the input dataset's display name appended to the new
history's name instead of plain numbers when the "Send results in a new
history" option is checked?
This new feature is indeed veeeeery useful (thanks a million for it) but the numbered
suffixes make it hard to track what new history belongs to which dataset.
Thanks,
L-A
Le 06/02/2012 23:00, Dannon Baker a écrit :
> This method only works for single inputs at the moment, though eventually it'd be
nice to allow pairing. Another option for you would be to use the workflows API, with
which you can definitely specify multiple inputs. See workflow_execute.py in the
scripts/api folder of your galaxy installation for one method of doing this.
>
> -Dannon
>
>
> On Feb 6, 2012, at 4:53 PM, Dave Lin wrote:
>
>> Thank you Dannon. That is helpful.
>>
>>
>> What if I need to specify multiple inputs per run (i.e. .csfasta + .qual file)?
>>
>> -Dave
>>
>> On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker<dannonbaker(a)me.com> wrote:
>> Hi Dave,
>>
>> Yes, galaxy's standard run-workflow dialog has a feature where you can select
multiple datasets as input for a single "Input Dataset" step. To do this, click
the icon referenced by the tooltip in the screenshot below to select multiple files. All
parameters remain static between executions except for the single input dataset that gets
modified for each run, and that only one input dataset can be set to multiple files in
this fashion.
>>
>> -Dannon
>>
>> <PastedGraphic-2.png>
>>
>>
>>
>>
>>
>> On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:
>>
>>> Hi All,
>>>
>>> I'm looking to batch process 40 large data sets with the same galaxy
workflow.
>>>
>>> This obviously can be done in a brute-force manual manner.
>>>
>>> However, is there a better way to schedule/invoke these jobs in batch
>>>
>>> 1) from the UI with a plugin
>>> 2) command-line
>>> 3) web-service
>>>
>>> Thanks in advance for any pointers.
>>> Dave
>>>
>>> ___________________________________________________________
>>> 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/
>>
> ___________________________________________________________
> 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/
7:19 a.m.
New subject: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
Dannon Baker <dannonbaker@...> writes:
Hi Dave,
Yes, galaxy's standard run-workflow dialog has a feature where you can select
multiple datasets as input
for a single "Input Dataset" step. To do this, click the
icon referenced by
the tooltip in the screenshot
below to select multiple files. All parameters remain static between
executions except for the single
input dataset that gets modified for each run, and that only one
input dataset
can be set to multiple files
in this fashion.
-Dannon
Dannon,
what if I don't have this icon??? How can I enable this? Where is this
documented?
Thanks,
Bernd
4:45 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
In your workflows, are you using "Input Dataset" steps? Galaxy uses these steps
to know how to map datasets to do special things like this. If you're not currently
using them, just open the workflow editor and add input dataset steps (it's at the
very bottom of the tool list) connected to the tool inputs at the highest level of the
workflow, and you'll see the multiple dataset flagging when you go to run it next
time.
-Dannon
On Jul 4, 2012, at 3:19 AM, Bernd Jagla wrote:
Dannon Baker <dannonbaker@...> writes:
>
> Hi Dave,
>
> Yes, galaxy's standard run-workflow dialog has a feature where you can select
multiple datasets as input
> for a single "Input Dataset" step. To do this, click the icon referenced
by
the tooltip in the screenshot
> below to select multiple files. All parameters remain static between
executions except for the single
> input dataset that gets modified for each run, and that only one input dataset
can be set to multiple files
> in this fashion.
>
> -Dannon
Dannon,
what if I don't have this icon??? How can I enable this? Where is this
documented?
Thanks,
Bernd
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
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9:08 p.m.
New subject: Looking for recommendations: How to run galaxy workflows in batch
But this only works if you have a single dataset (such as a BAM file) for each workflow to
run on.
If you have pairs of files (such as paired end FASTQ files, not an uncommon workflow
nowadays :) ) you need to resort to using the API, since there is no support for paired
end sequencing in GALAXY in this batch processing from the UI (yet?). You can run the
Workflow one at a time, but you have to choose the FASTQ pairs your self.
I have written a fairly generic execution engine that I can share, that uses a config file
to describe the files you need from the library in simple key:value pairs and that can
execute the paired-end sequencing on hundreds of FASTQ files...It's a little hacky and
requires your FASTQ files to have some consistent naming for the forward and reverse reads
(_R1.fastq & _R2.fastq) but other than that it seems to do the job...
There is however a nasty bug in the API, in that it removes the files from your history if
you use them in the API (I will post something on that later) but it seems to work fine
for data in the libraries...
Thon
Regards,
Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeboer(a)me.com
LinkedIn Profile
On Jul 4, 2012, at 12:19 AM, Bernd Jagla wrote:
Dannon Baker <dannonbaker@...> writes:
>
> Hi Dave,
>
> Yes, galaxy's standard run-workflow dialog has a feature where you can select
multiple datasets as input
> for a single "Input Dataset" step. To do this, click the icon referenced
by
the tooltip in the screenshot
> below to select multiple files. All parameters remain static between
executions except for the single
> input dataset that gets modified for each run, and that only one input dataset
can be set to multiple files
> in this fashion.
>
> -Dannon
Dannon,
what if I don't have this icon??? How can I enable this? Where is this
documented?
Thanks,
Bernd
___________________________________________________________
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:
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3443
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3593
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galaxy-dev@lists.galaxyproject.org
8 comments
5 participants
participants (5)
-
Bernd Jagla -
Dannon Baker -
Dave Lin -
Louise-Amélie Schmitt -
Thon Deboer