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
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 _______________________________________________ galaxy-dev mailing list 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@ifom-ieo-campus.it */
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@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@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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@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@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@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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@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@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@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Thank you !
On Tue, Aug 24, 2010 at 5:06 PM, Nate Coraor nate@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@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@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@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
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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@ifom-ieo-campus.it */
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@ifom-ieo-campus.it */
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@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@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@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@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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@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@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@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@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
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Nate Coraor