galaxy-dist down?

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galaxy-dist down?

Leandro Hermida-2
Hi there,

For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
getting a 503 Service Temporarily Unavailable, is there a planned
maintenance?

best,
Leandro
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Re: galaxy-dist down?

Davide Cittaro

On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:

Hi there,

For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
getting a 503 Service Temporarily Unavailable, is there a planned
maintenance?


Same here! 

best,
Leandro
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/*
Davide Cittaro

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20139 Milano
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tel.: +39(02)574303007
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Re: galaxy-dist down?

Nate Coraor (nate@bx.psu.edu)
Davide Cittaro wrote:

>
> On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:
>
>> Hi there,
>>
>> For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
>> getting a 503 Service Temporarily Unavailable, is there a planned
>> maintenance?
>>
>
> Same here!

Thanks for reporting this, we're looking in to it.  It's not planned.

--nate

>
>> best,
>> Leandro
>> _______________________________________________
>> galaxy-dev mailing list
>> [hidden email] <mailto:[hidden email]>
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> /*
> Davide Cittaro
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: [hidden email]
> <mailto:[hidden email]>
> */
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

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Re: galaxy-dist down?

Leandro Hermida-2
Hi there,

Sorry to ask, is there another way I can currently download galaxy-dist?

best,
Leandro

On Mon, Aug 23, 2010 at 3:21 PM, Nate Coraor <[hidden email]> wrote:

> Davide Cittaro wrote:
>>
>> On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:
>>
>>> Hi there,
>>>
>>> For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
>>> getting a 503 Service Temporarily Unavailable, is there a planned
>>> maintenance?
>>>
>>
>> Same here!
>
> Thanks for reporting this, we're looking in to it.  It's not planned.
>
> --nate
>
>>
>>> best,
>>> Leandro
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> [hidden email] <mailto:[hidden email]>
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> /*
>> Davide Cittaro
>>
>> Cogentech - Consortium for Genomic Technologies
>> via adamello, 16
>> 20139 Milano
>> Italy
>>
>> tel.: +39(02)574303007
>> e-mail: [hidden email]
>> <mailto:[hidden email]>
>> */
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> galaxy-dev mailing list
>> [hidden email]
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>

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Re: galaxy-dist down?

Nate Coraor (nate@bx.psu.edu)
Leandro Hermida wrote:
> Hi there,
>
> Sorry to ask, is there another way I can currently download galaxy-dist?

Hi Leandro,

You can do so with:

hg pull -u -r 60448575467f http://bitbucket.org/galaxy/galaxy-central

--nate

>
> best,
> Leandro
>
> On Mon, Aug 23, 2010 at 3:21 PM, Nate Coraor <[hidden email]> wrote:
>> Davide Cittaro wrote:
>>> On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:
>>>
>>>> Hi there,
>>>>
>>>> For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
>>>> getting a 503 Service Temporarily Unavailable, is there a planned
>>>> maintenance?
>>>>
>>> Same here!
>> Thanks for reporting this, we're looking in to it.  It's not planned.
>>
>> --nate
>>
>>>> best,
>>>> Leandro
>>>> _______________________________________________
>>>> galaxy-dev mailing list
>>>> [hidden email] <mailto:[hidden email]>
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>> /*
>>> Davide Cittaro
>>>
>>> Cogentech - Consortium for Genomic Technologies
>>> via adamello, 16
>>> 20139 Milano
>>> Italy
>>>
>>> tel.: +39(02)574303007
>>> e-mail: [hidden email]
>>> <mailto:[hidden email]>
>>> */
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> [hidden email]
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>

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Re: galaxy-dist down?

Leandro Hermida-2
Thank you !

On Tue, Aug 24, 2010 at 5:06 PM, Nate Coraor <[hidden email]> wrote:

> Leandro Hermida wrote:
>>
>> Hi there,
>>
>> Sorry to ask, is there another way I can currently download galaxy-dist?
>
> Hi Leandro,
>
> You can do so with:
>
> hg pull -u -r 60448575467f http://bitbucket.org/galaxy/galaxy-central
>
> --nate
>
>>
>> best,
>> Leandro
>>
>> On Mon, Aug 23, 2010 at 3:21 PM, Nate Coraor <[hidden email]> wrote:
>>>
>>> Davide Cittaro wrote:
>>>>
>>>> On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:
>>>>
>>>>> Hi there,
>>>>>
>>>>> For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
>>>>> getting a 503 Service Temporarily Unavailable, is there a planned
>>>>> maintenance?
>>>>>
>>>> Same here!
>>>
>>> Thanks for reporting this, we're looking in to it.  It's not planned.
>>>
>>> --nate
>>>
>>>>> best,
>>>>> Leandro
>>>>> _______________________________________________
>>>>> galaxy-dev mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>
>>>> /*
>>>> Davide Cittaro
>>>>
>>>> Cogentech - Consortium for Genomic Technologies
>>>> via adamello, 16
>>>> 20139 Milano
>>>> Italy
>>>>
>>>> tel.: +39(02)574303007
>>>> e-mail: [hidden email]
>>>> <mailto:[hidden email]>
>>>> */
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> galaxy-dev mailing list
>>>> [hidden email]
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
>>
>
>

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Re: galaxy-dist down?

Davide Cittaro
In reply to this post by Nate Coraor (nate@bx.psu.edu)

On Aug 24, 2010, at 5:06 PM, Nate Coraor wrote:
Hi Leandro,

You can do so with:

hg pull -u -r 60448575467f http://bitbucket.org/galaxy/galaxy-central


Mmm... after the upgrade and restart of the instance I get:

$ sh manage_db.sh upgrade
51 -> 52... 

Migration script to add the sample_dataset table and remove the 'dataset_files' column 
from the 'sample' table

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 55, in <module>
    main( repository=repo, url=db_url )
  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
    ret = command_func(**kwargs)
  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange
    change.run(self.engine, step)
  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run
    func()
  File "lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py", line 65, in upgrade
    dataset_files = from_json_string(r[1])
  File "/data/galaxy_dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_64-ucs2.egg/simplejson/__init__.py", line 384, in loads
  File "/data/galaxy_dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_64-ucs2.egg/simplejson/decoder.py", line 402, in decode
  File "/data/galaxy_dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_64-ucs2.egg/simplejson/decoder.py", line 418, in raw_decode
TypeError: first argument must be a string, not buffer


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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Re: galaxy-dist down?

Davide Cittaro

On Aug 24, 2010, at 6:12 PM, Davide Cittaro wrote:


On Aug 24, 2010, at 5:06 PM, Nate Coraor wrote:
Hi Leandro,

You can do so with:

hg pull -u -r 60448575467f http://bitbucket.org/galaxy/galaxy-central


Mmm... after the upgrade and restart of the instance I get:

$ sh manage_db.sh upgrade
51 -> 52... 


Ive solved changing line 65 in 0052 upgrade script into this:


if r[1] and type(r[1]) is str:

The result of the query was pretty empty, anyway:

# SELECT id, dataset_files FROM sample; 
 id | dataset_files 
----+---------------
  3 | []
  4 | []
  5 | []
  1 | []
  2 | []
(5 rows)


After this upgrade I still have issues with bigwig and UCSC... I'll send a separate mail, tomorrow...

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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Re: galaxy-dist down?

Leandro Hermida-2
In reply to this post by Nate Coraor (nate@bx.psu.edu)
Hi,

For the pull listed it said I needed an existing repository and
aborted, so I did this is this equivalent?

hg clone -r 60448575467f http://bitbucket.org/galaxy/galaxy-central galaxy-dist

Leandro

On Tue, Aug 24, 2010 at 5:06 PM, Nate Coraor <[hidden email]> wrote:

> Leandro Hermida wrote:
>>
>> Hi there,
>>
>> Sorry to ask, is there another way I can currently download galaxy-dist?
>
> Hi Leandro,
>
> You can do so with:
>
> hg pull -u -r 60448575467f http://bitbucket.org/galaxy/galaxy-central
>
> --nate
>
>>
>> best,
>> Leandro
>>
>> On Mon, Aug 23, 2010 at 3:21 PM, Nate Coraor <[hidden email]> wrote:
>>>
>>> Davide Cittaro wrote:
>>>>
>>>> On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:
>>>>
>>>>> Hi there,
>>>>>
>>>>> For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
>>>>> getting a 503 Service Temporarily Unavailable, is there a planned
>>>>> maintenance?
>>>>>
>>>> Same here!
>>>
>>> Thanks for reporting this, we're looking in to it.  It's not planned.
>>>
>>> --nate
>>>
>>>>> best,
>>>>> Leandro
>>>>> _______________________________________________
>>>>> galaxy-dev mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>
>>>> /*
>>>> Davide Cittaro
>>>>
>>>> Cogentech - Consortium for Genomic Technologies
>>>> via adamello, 16
>>>> 20139 Milano
>>>> Italy
>>>>
>>>> tel.: +39(02)574303007
>>>> e-mail: [hidden email]
>>>> <mailto:[hidden email]>
>>>> */
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> galaxy-dev mailing list
>>>> [hidden email]
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
>>
>
>

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Re: galaxy-dist down?

Nate Coraor (nate@bx.psu.edu)
Leandro Hermida wrote:
> Hi,
>
> For the pull listed it said I needed an existing repository and
> aborted, so I did this is this equivalent?
>
> hg clone -r 60448575467f http://bitbucket.org/galaxy/galaxy-central galaxy-dist

Ah yes, this is fine, I assumed you were updating an existing repo.
When the galaxy-dist repo is back up, you will probably want to modify
galaxy-dist/.hg/hgrc to point to it.

--nate

>
> Leandro
>
> On Tue, Aug 24, 2010 at 5:06 PM, Nate Coraor <[hidden email]> wrote:
>> Leandro Hermida wrote:
>>> Hi there,
>>>
>>> Sorry to ask, is there another way I can currently download galaxy-dist?
>> Hi Leandro,
>>
>> You can do so with:
>>
>> hg pull -u -r 60448575467f http://bitbucket.org/galaxy/galaxy-central
>>
>> --nate
>>
>>> best,
>>> Leandro
>>>
>>> On Mon, Aug 23, 2010 at 3:21 PM, Nate Coraor <[hidden email]> wrote:
>>>> Davide Cittaro wrote:
>>>>> On Aug 23, 2010, at 11:36 AM, Leandro Hermida wrote:
>>>>>
>>>>>> Hi there,
>>>>>>
>>>>>> For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am
>>>>>> getting a 503 Service Temporarily Unavailable, is there a planned
>>>>>> maintenance?
>>>>>>
>>>>> Same here!
>>>> Thanks for reporting this, we're looking in to it.  It's not planned.
>>>>
>>>> --nate
>>>>
>>>>>> best,
>>>>>> Leandro
>>>>>> _______________________________________________
>>>>>> galaxy-dev mailing list
>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>> /*
>>>>> Davide Cittaro
>>>>>
>>>>> Cogentech - Consortium for Genomic Technologies
>>>>> via adamello, 16
>>>>> 20139 Milano
>>>>> Italy
>>>>>
>>>>> tel.: +39(02)574303007
>>>>> e-mail: [hidden email]
>>>>> <mailto:[hidden email]>
>>>>> */
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> galaxy-dev mailing list
>>>>> [hidden email]
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>

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