Toolshed bug related to readme files

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Toolshed bug related to readme files

Lance Parsons
I have run into an issue when trying to reinstall a tool that was
originally installed via migration scripts (toolshed version of picard).

When I attempt to reinstall (after successfully uninstalling) I get a
500 error.  After a bit of poking around, it seems that this URL
generates the 500 error:

http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965

Looks like this changeset is relevant:
https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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Re: Toolshed bug related to readme files

Greg Von Kuster
Hi Lance,

What version of Galaxy are you running?  Is the 500 error coming from your Galaxy server or the tool shed server?  Can you send the relevant information from your Galaxy paster log when attempting to reinstall?

Thanks,

Greg Von Kuster


On Jun 11, 2013, at 3:52 PM, Lance Parsons <[hidden email]> wrote:

> I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard).
>
> When I attempt to reinstall (after successfully uninstalling) I get a 500 error.  After a bit of poking around, it seems that this URL generates the 500 error:
>
> http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
>
> Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
>
>
> --
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/


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Re: Toolshed bug related to readme files

Lance Parsons
In reply to this post by Lance Parsons
I'm running the latest stable.

The 500 error seems to be coming from the toolshed. Do you also get a 500 error at the toolshed URL in my previous message? 

There is nothing other than standard info line from the request in my pasted log. I'm not able to get to the log right now, but I'll send it once I get a chance tomorrow.


-- 
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University



-------- Original message --------
From: Greg Von Kuster <[hidden email]>
Date: 06/11/2013 10:00 PM (GMT-05:00)
To: Lance Parsons <[hidden email]>
Cc: [hidden email]
Subject: Re: [galaxy-dev] Toolshed bug related to readme files


Hi Lance,

What version of Galaxy are you running?  Is the 500 error coming from your Galaxy server or the tool shed server?  Can you send the relevant information from your Galaxy paster log when attempting to reinstall?

Thanks,

Greg Von Kuster


On Jun 11, 2013, at 3:52 PM, Lance Parsons <[hidden email]> wrote:

> I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard).
>
> When I attempt to reinstall (after successfully uninstalling) I get a 500 error.  After a bit of poking around, it seems that this URL generates the 500 error:
>
> http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
>
> Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
>
>
> --
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/



___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
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Re: Toolshed bug related to readme files

Greg Von Kuster
Hi Lance,

Thanks for the information - I'll have a fix out shortly.

Greg Von Kuster

On Jun 11, 2013, at 10:12 PM, Lance Parsons <[hidden email]> wrote:

> I'm running the latest stable.
>
> The 500 error seems to be coming from the toolshed. Do you also get a 500 error at the toolshed URL in my previous message?
>
> There is nothing other than standard info line from the request in my pasted log. I'm not able to get to the log right now, but I'll send it once I get a chance tomorrow.
>
>
> --
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
>
>
> -------- Original message --------
> From: Greg Von Kuster <[hidden email]>
> Date: 06/11/2013 10:00 PM (GMT-05:00)
> To: Lance Parsons <[hidden email]>
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] Toolshed bug related to readme files
>
>
> Hi Lance,
>
> What version of Galaxy are you running?  Is the 500 error coming from your Galaxy server or the tool shed server?  Can you send the relevant information from your Galaxy paster log when attempting to reinstall?
>
> Thanks,
>
> Greg Von Kuster
>
>
> On Jun 11, 2013, at 3:52 PM, Lance Parsons <[hidden email]> wrote:
>
> > I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard).
> >
> > When I attempt to reinstall (after successfully uninstalling) I get a 500 error.  After a bit of poking around, it seems that this URL generates the 500 error:
> >
> > http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
> >
> > Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
> >
> >
> > --
> > Lance Parsons - Scientific Programmer
> > 134 Carl C. Icahn Laboratory
> > Lewis-Sigler Institute for Integrative Genomics
> > Princeton University
> >
> > ___________________________________________________________
> > 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/
> >
> > To search Galaxy mailing lists use the unified search at:
> > http://galaxyproject.org/search/mailinglists/
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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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Re: Toolshed bug related to readme files

Greg Von Kuster
Hello Lance,

This issue should be corrected in change set 9994:f8cf776ff12f, which is currently running on both public tool sheds.  Thanks for reporting this!

Greg Von Kuster

On Jun 12, 2013, at 6:25 AM, Greg Von Kuster <[hidden email]> wrote:

> Hi Lance,
>
> Thanks for the information - I'll have a fix out shortly.
>
> Greg Von Kuster
>
> On Jun 11, 2013, at 10:12 PM, Lance Parsons <[hidden email]> wrote:
>
>> I'm running the latest stable.
>>
>> The 500 error seems to be coming from the toolshed. Do you also get a 500 error at the toolshed URL in my previous message?
>>
>> There is nothing other than standard info line from the request in my pasted log. I'm not able to get to the log right now, but I'll send it once I get a chance tomorrow.
>>
>>
>> --
>> Lance Parsons - Scientific Programmer
>> 134 Carl C. Icahn Laboratory
>> Lewis-Sigler Institute for Integrative Genomics
>> Princeton University
>>
>>
>>
>> -------- Original message --------
>> From: Greg Von Kuster <[hidden email]>
>> Date: 06/11/2013 10:00 PM (GMT-05:00)
>> To: Lance Parsons <[hidden email]>
>> Cc: [hidden email]
>> Subject: Re: [galaxy-dev] Toolshed bug related to readme files
>>
>>
>> Hi Lance,
>>
>> What version of Galaxy are you running?  Is the 500 error coming from your Galaxy server or the tool shed server?  Can you send the relevant information from your Galaxy paster log when attempting to reinstall?
>>
>> Thanks,
>>
>> Greg Von Kuster
>>
>>
>> On Jun 11, 2013, at 3:52 PM, Lance Parsons <[hidden email]> wrote:
>>
>>> I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard).
>>>
>>> When I attempt to reinstall (after successfully uninstalling) I get a 500 error.  After a bit of poking around, it seems that this URL generates the 500 error:
>>>
>>> http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
>>>
>>> Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
>>>
>>>
>>> --
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>
>>
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/