Problems saving workflow that includes 'manipulate fastq'

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Problems saving workflow that includes 'manipulate fastq'

Pip Griffin
I attempted to post this message to the list a week ago, but haven't
had any replies, so may not have posted it properly.

I am making a workflow without having actual data to test it on yet.
When I include even a (seemingly simple) 'manipulate fastq' step, and
save the workflow, it tries to save for many minutes, unsuccessfully,
until I get sick of it and close the window.

Can someone please tell me if there's something I can do about this?

thanks
Pip Griffin
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Re: Problems saving workflow that includes 'manipulate fastq'

Jeremy Goecks
Hi Pip,

Sorry for the slow reply.

Answering a couple questions will help us diagnose your problem:

*are you making this workflow on your local galaxy instance or on our public (main) webserver?
*do all workflows that include the 'manipulate fastq' step fail? (e.g. if you create a new workflow with simply an input dataset and manipulate fastq, does it fail to save?)

J.



On Jun 1, 2010, at 8:22 PM, Pip Griffin wrote:

> I attempted to post this message to the list a week ago, but haven't
> had any replies, so may not have posted it properly.
>
> I am making a workflow without having actual data to test it on yet.
> When I include even a (seemingly simple) 'manipulate fastq' step, and
> save the workflow, it tries to save for many minutes, unsuccessfully,
> until I get sick of it and close the window.
>
> Can someone please tell me if there's something I can do about this?
>
> thanks
> Pip Griffin
> _______________________________________________
> galaxy-user mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user


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Re: Problems saving workflow that includes 'manipulate fastq'

Pip Griffin
Hi Jeremy,

1) I am making the workflow on the public webserver.

2) I just made a simple workflow with three steps: data input (using
the 'example_human_454.fasta' and 'example_human_454.qv' files from
the website), followed by a 'combine fasta and qv to fastq' step,
followed by 'manipulate fastq' to match all lines containing a short
DNA sequence and reverse-complement them. It still failed to save...
It will save if I put in an empty 'manipulate fastq' step but as soon
as I enter any details at all into that step it fails to save. I've
tried various combinations of steps and nothing has worked so far.

thanks for your help

Pip


On Wed, Jun 2, 2010 at 1:11 PM, Jeremy Goecks <[hidden email]> wrote:

> Hi Pip,
>
> Sorry for the slow reply.
>
> Answering a couple questions will help us diagnose your problem:
>
> *are you making this workflow on your local galaxy instance or on our public (main) webserver?
> *do all workflows that include the 'manipulate fastq' step fail? (e.g. if you create a new workflow with simply an input dataset and manipulate fastq, does it fail to save?)
>
> J.
>
>
>
> On Jun 1, 2010, at 8:22 PM, Pip Griffin wrote:
>
>> I attempted to post this message to the list a week ago, but haven't
>> had any replies, so may not have posted it properly.
>>
>> I am making a workflow without having actual data to test it on yet.
>> When I include even a (seemingly simple) 'manipulate fastq' step, and
>> save the workflow, it tries to save for many minutes, unsuccessfully,
>> until I get sick of it and close the window.
>>
>> Can someone please tell me if there's something I can do about this?
>>
>> thanks
>> Pip Griffin
>> _______________________________________________
>> galaxy-user mailing list
>> [hidden email]
>> http://lists.bx.psu.edu/listinfo/galaxy-user
>
>
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Re: Problems saving workflow that includes 'manipulate fastq'

Jeremy Goecks
Hi Pip,

I can't seem to reproduce your error. Here's a workflow I created which performs the steps you discussed:

http://main.g2.bx.psu.edu/u/jgoecks/w/manipulate-fastq-test

Try importing the workflow into your workspace, modifying the 'manipulate fastq' step, and see if you can save it.

One possible explanation is that we updated our main server yesterday, and this may have fixed your problem. In any case, let us know if you're still having problems.

Best,
J.



On Jun 2, 2010, at 3:29 AM, Pip Griffin wrote:

> Hi Jeremy,
>
> 1) I am making the workflow on the public webserver.
>
> 2) I just made a simple workflow with three steps: data input (using
> the 'example_human_454.fasta' and 'example_human_454.qv' files from
> the website), followed by a 'combine fasta and qv to fastq' step,
> followed by 'manipulate fastq' to match all lines containing a short
> DNA sequence and reverse-complement them. It still failed to save...
> It will save if I put in an empty 'manipulate fastq' step but as soon
> as I enter any details at all into that step it fails to save. I've
> tried various combinations of steps and nothing has worked so far.
>
> thanks for your help
>
> Pip
>
>
> On Wed, Jun 2, 2010 at 1:11 PM, Jeremy Goecks <[hidden email]> wrote:
>> Hi Pip,
>>
>> Sorry for the slow reply.
>>
>> Answering a couple questions will help us diagnose your problem:
>>
>> *are you making this workflow on your local galaxy instance or on our public (main) webserver?
>> *do all workflows that include the 'manipulate fastq' step fail? (e.g. if you create a new workflow with simply an input dataset and manipulate fastq, does it fail to save?)
>>
>> J.
>>
>>
>>
>> On Jun 1, 2010, at 8:22 PM, Pip Griffin wrote:
>>
>>> I attempted to post this message to the list a week ago, but haven't
>>> had any replies, so may not have posted it properly.
>>>
>>> I am making a workflow without having actual data to test it on yet.
>>> When I include even a (seemingly simple) 'manipulate fastq' step, and
>>> save the workflow, it tries to save for many minutes, unsuccessfully,
>>> until I get sick of it and close the window.
>>>
>>> Can someone please tell me if there's something I can do about this?
>>>
>>> thanks
>>> Pip Griffin
>>> _______________________________________________
>>> galaxy-user mailing list
>>> [hidden email]
>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>>


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Re: Problems saving workflow that includes 'manipulate fastq'

Jelle Scholtalbers
Hi,

which browser are you actually using? As I have noticed that MS IE is
not always working nice with Galaxy (for example I can't edit any
steps in the workflow editor at the Galaxy test instance).If you were
using IE, try to switch to another browser and it might just work.

Might be related to:
http://bitbucket.org/galaxy/galaxy-central/issue/166/workflow-canvas-issue-in-ie-solved-by-installing

Cheers,
Jelle

On Wed, Jun 2, 2010 at 3:46 PM, Jeremy Goecks <[hidden email]> wrote:

> Hi Pip,
>
> I can't seem to reproduce your error. Here's a workflow I created which performs the steps you discussed:
>
> http://main.g2.bx.psu.edu/u/jgoecks/w/manipulate-fastq-test
>
> Try importing the workflow into your workspace, modifying the 'manipulate fastq' step, and see if you can save it.
>
> One possible explanation is that we updated our main server yesterday, and this may have fixed your problem. In any case, let us know if you're still having problems.
>
> Best,
> J.
>
>
>
> On Jun 2, 2010, at 3:29 AM, Pip Griffin wrote:
>
>> Hi Jeremy,
>>
>> 1) I am making the workflow on the public webserver.
>>
>> 2) I just made a simple workflow with three steps: data input (using
>> the 'example_human_454.fasta' and 'example_human_454.qv' files from
>> the website), followed by a 'combine fasta and qv to fastq' step,
>> followed by 'manipulate fastq' to match all lines containing a short
>> DNA sequence and reverse-complement them. It still failed to save...
>> It will save if I put in an empty 'manipulate fastq' step but as soon
>> as I enter any details at all into that step it fails to save. I've
>> tried various combinations of steps and nothing has worked so far.
>>
>> thanks for your help
>>
>> Pip
>>
>>
>> On Wed, Jun 2, 2010 at 1:11 PM, Jeremy Goecks <[hidden email]> wrote:
>>> Hi Pip,
>>>
>>> Sorry for the slow reply.
>>>
>>> Answering a couple questions will help us diagnose your problem:
>>>
>>> *are you making this workflow on your local galaxy instance or on our public (main) webserver?
>>> *do all workflows that include the 'manipulate fastq' step fail? (e.g. if you create a new workflow with simply an input dataset and manipulate fastq, does it fail to save?)
>>>
>>> J.
>>>
>>>
>>>
>>> On Jun 1, 2010, at 8:22 PM, Pip Griffin wrote:
>>>
>>>> I attempted to post this message to the list a week ago, but haven't
>>>> had any replies, so may not have posted it properly.
>>>>
>>>> I am making a workflow without having actual data to test it on yet.
>>>> When I include even a (seemingly simple) 'manipulate fastq' step, and
>>>> save the workflow, it tries to save for many minutes, unsuccessfully,
>>>> until I get sick of it and close the window.
>>>>
>>>> Can someone please tell me if there's something I can do about this?
>>>>
>>>> thanks
>>>> Pip Griffin
>>>> _______________________________________________
>>>> galaxy-user mailing list
>>>> [hidden email]
>>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>
>>>
>
>
> _______________________________________________
> galaxy-user mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user
>
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Re: Problems saving workflow that includes 'manipulate fastq'

Pip Griffin
Well this is quite mysterious. I had no problems with altering and
saving the 'manipulate fastq' step already in your workflow, Jeremy,
but when I tried to add a second 'manipulate fastq' step, it still
failed to save. Also the problem is still there with my workflow.
Maybe you can work out what's wrong if you have a look at it:

http://main.g2.bx.psu.edu/u/pgriffin/w/workflow-from-example-human-dataset

I'm using Firefox, so it can't be an IE issue either.

thanks
Pip




On Thu, Jun 3, 2010 at 12:31 AM, Jelle Scholtalbers
<[hidden email]> wrote:

> Hi,
>
> which browser are you actually using? As I have noticed that MS IE is
> not always working nice with Galaxy (for example I can't edit any
> steps in the workflow editor at the Galaxy test instance).If you were
> using IE, try to switch to another browser and it might just work.
>
> Might be related to:
> http://bitbucket.org/galaxy/galaxy-central/issue/166/workflow-canvas-issue-in-ie-solved-by-installing
>
> Cheers,
> Jelle
>
> On Wed, Jun 2, 2010 at 3:46 PM, Jeremy Goecks <[hidden email]> wrote:
>> Hi Pip,
>>
>> I can't seem to reproduce your error. Here's a workflow I created which performs the steps you discussed:
>>
>> http://main.g2.bx.psu.edu/u/jgoecks/w/manipulate-fastq-test
>>
>> Try importing the workflow into your workspace, modifying the 'manipulate fastq' step, and see if you can save it.
>>
>> One possible explanation is that we updated our main server yesterday, and this may have fixed your problem. In any case, let us know if you're still having problems.
>>
>> Best,
>> J.
>>
>>
>>
>> On Jun 2, 2010, at 3:29 AM, Pip Griffin wrote:
>>
>>> Hi Jeremy,
>>>
>>> 1) I am making the workflow on the public webserver.
>>>
>>> 2) I just made a simple workflow with three steps: data input (using
>>> the 'example_human_454.fasta' and 'example_human_454.qv' files from
>>> the website), followed by a 'combine fasta and qv to fastq' step,
>>> followed by 'manipulate fastq' to match all lines containing a short
>>> DNA sequence and reverse-complement them. It still failed to save...
>>> It will save if I put in an empty 'manipulate fastq' step but as soon
>>> as I enter any details at all into that step it fails to save. I've
>>> tried various combinations of steps and nothing has worked so far.
>>>
>>> thanks for your help
>>>
>>> Pip
>>>
>>>
>>> On Wed, Jun 2, 2010 at 1:11 PM, Jeremy Goecks <[hidden email]> wrote:
>>>> Hi Pip,
>>>>
>>>> Sorry for the slow reply.
>>>>
>>>> Answering a couple questions will help us diagnose your problem:
>>>>
>>>> *are you making this workflow on your local galaxy instance or on our public (main) webserver?
>>>> *do all workflows that include the 'manipulate fastq' step fail? (e.g. if you create a new workflow with simply an input dataset and manipulate fastq, does it fail to save?)
>>>>
>>>> J.
>>>>
>>>>
>>>>
>>>> On Jun 1, 2010, at 8:22 PM, Pip Griffin wrote:
>>>>
>>>>> I attempted to post this message to the list a week ago, but haven't
>>>>> had any replies, so may not have posted it properly.
>>>>>
>>>>> I am making a workflow without having actual data to test it on yet.
>>>>> When I include even a (seemingly simple) 'manipulate fastq' step, and
>>>>> save the workflow, it tries to save for many minutes, unsuccessfully,
>>>>> until I get sick of it and close the window.
>>>>>
>>>>> Can someone please tell me if there's something I can do about this?
>>>>>
>>>>> thanks
>>>>> Pip Griffin
>>>>> _______________________________________________
>>>>> galaxy-user mailing list
>>>>> [hidden email]
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>>
>>>>
>>
>>
>> _______________________________________________
>> galaxy-user mailing list
>> [hidden email]
>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>
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Re: Problems saving workflow that includes 'manipulate fastq'

Jeremy Goecks
Hi Pip,

We've been able to replicate your error but are still working to fix it. We suspect that the problem is Firefox specific, so you might be able to make progress with your workflow if you could use another browser such as Safari or Chrome.

We'll let you know when we've resolved the problem.

Thanks,
J.



On Jun 2, 2010, at 8:52 PM, Pip Griffin wrote:

> Well this is quite mysterious. I had no problems with altering and
> saving the 'manipulate fastq' step already in your workflow, Jeremy,
> but when I tried to add a second 'manipulate fastq' step, it still
> failed to save. Also the problem is still there with my workflow.
> Maybe you can work out what's wrong if you have a look at it:
>
> http://main.g2.bx.psu.edu/u/pgriffin/w/workflow-from-example-human-dataset
>
> I'm using Firefox, so it can't be an IE issue either.
>
> thanks
> Pip
>
>
>
>
> On Thu, Jun 3, 2010 at 12:31 AM, Jelle Scholtalbers
> <[hidden email]> wrote:
>> Hi,
>>
>> which browser are you actually using? As I have noticed that MS IE is
>> not always working nice with Galaxy (for example I can't edit any
>> steps in the workflow editor at the Galaxy test instance).If you were
>> using IE, try to switch to another browser and it might just work.
>>
>> Might be related to:
>> http://bitbucket.org/galaxy/galaxy-central/issue/166/workflow-canvas-issue-in-ie-solved-by-installing
>>
>> Cheers,
>> Jelle
>>
>> On Wed, Jun 2, 2010 at 3:46 PM, Jeremy Goecks <[hidden email]> wrote:
>>> Hi Pip,
>>>
>>> I can't seem to reproduce your error. Here's a workflow I created which performs the steps you discussed:
>>>
>>> http://main.g2.bx.psu.edu/u/jgoecks/w/manipulate-fastq-test
>>>
>>> Try importing the workflow into your workspace, modifying the 'manipulate fastq' step, and see if you can save it.
>>>
>>> One possible explanation is that we updated our main server yesterday, and this may have fixed your problem. In any case, let us know if you're still having problems.
>>>
>>> Best,
>>> J.
>>>
>>>
>>>
>>> On Jun 2, 2010, at 3:29 AM, Pip Griffin wrote:
>>>
>>>> Hi Jeremy,
>>>>
>>>> 1) I am making the workflow on the public webserver.
>>>>
>>>> 2) I just made a simple workflow with three steps: data input (using
>>>> the 'example_human_454.fasta' and 'example_human_454.qv' files from
>>>> the website), followed by a 'combine fasta and qv to fastq' step,
>>>> followed by 'manipulate fastq' to match all lines containing a short
>>>> DNA sequence and reverse-complement them. It still failed to save...
>>>> It will save if I put in an empty 'manipulate fastq' step but as soon
>>>> as I enter any details at all into that step it fails to save. I've
>>>> tried various combinations of steps and nothing has worked so far.
>>>>
>>>> thanks for your help
>>>>
>>>> Pip
>>>>
>>>>
>>>> On Wed, Jun 2, 2010 at 1:11 PM, Jeremy Goecks <[hidden email]> wrote:
>>>>> Hi Pip,
>>>>>
>>>>> Sorry for the slow reply.
>>>>>
>>>>> Answering a couple questions will help us diagnose your problem:
>>>>>
>>>>> *are you making this workflow on your local galaxy instance or on our public (main) webserver?
>>>>> *do all workflows that include the 'manipulate fastq' step fail? (e.g. if you create a new workflow with simply an input dataset and manipulate fastq, does it fail to save?)
>>>>>
>>>>> J.
>>>>>
>>>>>
>>>>>
>>>>> On Jun 1, 2010, at 8:22 PM, Pip Griffin wrote:
>>>>>
>>>>>> I attempted to post this message to the list a week ago, but haven't
>>>>>> had any replies, so may not have posted it properly.
>>>>>>
>>>>>> I am making a workflow without having actual data to test it on yet.
>>>>>> When I include even a (seemingly simple) 'manipulate fastq' step, and
>>>>>> save the workflow, it tries to save for many minutes, unsuccessfully,
>>>>>> until I get sick of it and close the window.
>>>>>>
>>>>>> Can someone please tell me if there's something I can do about this?
>>>>>>
>>>>>> thanks
>>>>>> Pip Griffin
>>>>>> _______________________________________________
>>>>>> galaxy-user mailing list
>>>>>> [hidden email]
>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>>>
>>>>>
>>>
>>>
>>> _______________________________________________
>>> galaxy-user mailing list
>>> [hidden email]
>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>
>>


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Re: Problems saving workflow that includes 'manipulate fastq'

Kanwei Li
In reply to this post by Pip Griffin
Hi Pip,

This has been fixed in commit 3875. Thanks for reporting the bug.

Kanwei

On Wed, Jun 2, 2010 at 8:52 PM, Pip Griffin <[hidden email]> wrote:

> Well this is quite mysterious. I had no problems with altering and
> saving the 'manipulate fastq' step already in your workflow, Jeremy,
> but when I tried to add a second 'manipulate fastq' step, it still
> failed to save. Also the problem is still there with my workflow.
> Maybe you can work out what's wrong if you have a look at it:
>
> http://main.g2.bx.psu.edu/u/pgriffin/w/workflow-from-example-human-dataset
>
> I'm using Firefox, so it can't be an IE issue either.
>
> thanks
> Pip
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Re: Problems saving workflow that includes 'manipulate fastq'

Pip Griffin
Thanks! It's working fine now.

Pip

On Sat, Jun 5, 2010 at 8:29 AM, Kanwei Li <[hidden email]> wrote:

> Hi Pip,
>
> This has been fixed in commit 3875. Thanks for reporting the bug.
>
> Kanwei
>
> On Wed, Jun 2, 2010 at 8:52 PM, Pip Griffin <[hidden email]> wrote:
>> Well this is quite mysterious. I had no problems with altering and
>> saving the 'manipulate fastq' step already in your workflow, Jeremy,
>> but when I tried to add a second 'manipulate fastq' step, it still
>> failed to save. Also the problem is still there with my workflow.
>> Maybe you can work out what's wrong if you have a look at it:
>>
>> http://main.g2.bx.psu.edu/u/pgriffin/w/workflow-from-example-human-dataset
>>
>> I'm using Firefox, so it can't be an IE issue either.
>>
>> thanks
>> Pip
>
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