9:36 a.m.
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
9:40 a.m.
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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galaxy-dev mailing list
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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: davide.cittaro(a)ifom-ieo-campus.it
*/
1:21 p.m.
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
> galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
> 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: davide.cittaro(a)ifom-ieo-campus.it
<mailto:davide.cittaro@ifom-ieo-campus.it>
*/
------------------------------------------------------------------------
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2:56 p.m.
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 <nate(a)bx.psu.edu> 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
>> galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
>> 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: davide.cittaro(a)ifom-ieo-campus.it
> <mailto:davide.cittaro@ifom-ieo-campus.it>
> */
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
3:06 p.m.
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 <nate(a)bx.psu.edu> 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
>>> galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
>>> 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: davide.cittaro(a)ifom-ieo-campus.it
>> <mailto:davide.cittaro@ifom-ieo-campus.it>
>> */
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
3:33 p.m.
Thank you !
On Tue, Aug 24, 2010 at 5:06 PM, Nate Coraor <nate(a)bx.psu.edu> 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 <nate(a)bx.psu.edu> 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
>>>> galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
>>>> 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: davide.cittaro(a)ifom-ieo-campus.it
>>> <mailto:davide.cittaro@ifom-ieo-campus.it>
>>> */
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>
4:12 p.m.
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
e-mail: davide.cittaro(a)ifom-ieo-campus.it
*/
4:50 p.m.
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
e-mail: davide.cittaro(a)ifom-ieo-campus.it
*/
6:04 p.m.
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 <nate(a)bx.psu.edu> 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 <nate(a)bx.psu.edu> 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
>>>> galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
>>>> 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: davide.cittaro(a)ifom-ieo-campus.it
>>> <mailto:davide.cittaro@ifom-ieo-campus.it>
>>> */
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>
6:06 p.m.
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 <nate(a)bx.psu.edu> 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 <nate(a)bx.psu.edu> 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
>>>>> galaxy-dev(a)lists.bx.psu.edu
<mailto:galaxy-dev@lists.bx.psu.edu>
>>>>> 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: davide.cittaro(a)ifom-ieo-campus.it
>>>> <mailto:davide.cittaro@ifom-ieo-campus.it>
>>>> */
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> galaxy-dev mailing list
>>>> galaxy-dev(a)lists.bx.psu.edu
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
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9 comments
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participants (3)
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Nate Coraor