Re: [galaxy-dev] Urgent help needed
?That's what I wanted to hear! Thanks a lot once again. Best, Marija Von: Nate Coraor Gesendet: Donnerstag, 19. Oktober 2017 18:59 An: Durdevic, Marija Cc: galaxy-dev@lists.galaxyproject.org Betreff: Re: [galaxy-dev] Urgent help needed Ah ok, this is good news, then. Other than your local changes, you can just clone Galaxy again and start it with your old configs and database. --nate On Thu, Oct 19, 2017 at 12:57 PM, Durdevic, Marija mailto:marija.durde...@medunigraz.at>> wrote: ?Hi Nate, Thanks a lot for your prompt response! I stopped all the services immediately, umount the volume and run recovery. It will take some time and hopefully I will have some results tomorrow. In case not, I am asking for the worst case scenario. Luckily, galaxy database, all datasets, tool_shed and all tools were on another location, so I still have them. He deleted only galaxy directory. Of course, I had some local tools an wrappers there, but at least I hope I can still do something. Thanks once again! Best, Marija Von: Nate Coraor mailto:n...@bx.psu.edu>> Gesendet: Donnerstag, 19. Oktober 2017 18:36 An: Durdevic, Marija Cc: galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Betreff: Re: [galaxy-dev] Urgent help needed Hi Marija, Wow, sorry to hear this. If the datasets themselves were removed, it's unlikely there'd be a way to get them back. Some filesystems do have undelete tools to attempt to recover data that has not yet been overwritten. If you can stop all activity on that filesystem while investigating and attempt to recover, this would likely increase the amount of data you'd be able to recover. It would be possible to reconnect to the database assuming it was not SQLite and also removed. Your existing backed up configs should do this automatically. This would restore your users and their Galaxy representations of things, such as histories, but without the actual data in those histories. --nate On Thu, Oct 19, 2017 at 10:32 AM, Durdevic, Marija mailto:marija.durde...@medunigraz.at>> wrote: Dear developers, The colleague of mine mistakenly deleted my Galaxy installation (rm -rf *). Unfortunately there is no backup of complete installation. I have backup only configuration files. Is there any chance to fetch new Galaxy instance from git and to connect it to the old database? Or maybe any other suggestion what to do in such case? Many thanks in advance! Best, Marija Mag. Marija Durdevic Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24<https://maps.google.com/?q=Stiftingtalstra%C3%9Fe+24&entry=gmail&source=g>, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.durde...@medunigraz.at<mailto:marija.durde...@medunigraz.at> Email: marija.djurdje...@klinikum-graz.at<mailto:marija.djurdje...@klinikum-graz.at> Web: https://zmf.medunigraz.at/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Urgent help needed
?Hi Nate, Thanks a lot for your prompt response! I stopped all the services immediately, umount the volume and run recovery. It will take some time and hopefully I will have some results tomorrow. In case not, I am asking for the worst case scenario. Luckily, galaxy database, all datasets, tool_shed and all tools were on another location, so I still have them. He deleted only galaxy directory. Of course, I had some local tools an wrappers there, but at least I hope I can still do something. Thanks once again! Best, Marija Von: Nate Coraor Gesendet: Donnerstag, 19. Oktober 2017 18:36 An: Durdevic, Marija Cc: galaxy-dev@lists.galaxyproject.org Betreff: Re: [galaxy-dev] Urgent help needed Hi Marija, Wow, sorry to hear this. If the datasets themselves were removed, it's unlikely there'd be a way to get them back. Some filesystems do have undelete tools to attempt to recover data that has not yet been overwritten. If you can stop all activity on that filesystem while investigating and attempt to recover, this would likely increase the amount of data you'd be able to recover. It would be possible to reconnect to the database assuming it was not SQLite and also removed. Your existing backed up configs should do this automatically. This would restore your users and their Galaxy representations of things, such as histories, but without the actual data in those histories. --nate On Thu, Oct 19, 2017 at 10:32 AM, Durdevic, Marija mailto:marija.durde...@medunigraz.at>> wrote: Dear developers, The colleague of mine mistakenly deleted my Galaxy installation (rm -rf *). Unfortunately there is no backup of complete installation. I have backup only configuration files. Is there any chance to fetch new Galaxy instance from git and to connect it to the old database? Or maybe any other suggestion what to do in such case? Many thanks in advance! Best, Marija Mag. Marija Durdevic Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.durde...@medunigraz.at<mailto:marija.durde...@medunigraz.at> Email: marija.djurdje...@klinikum-graz.at<mailto:marija.djurdje...@klinikum-graz.at> Web: https://zmf.medunigraz.at/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Urgent help needed
Ah ok, this is good news, then. Other than your local changes, you can just clone Galaxy again and start it with your old configs and database. --nate On Thu, Oct 19, 2017 at 12:57 PM, Durdevic, Marija < marija.durde...@medunigraz.at> wrote: > Hi Nate, > > > Thanks a lot for your prompt response! > > > I stopped all the services immediately, umount the volume and run > recovery. It will take some time and hopefully I will have some results > tomorrow. > > In case not, I am asking for the worst case scenario. > > Luckily, galaxy database, all datasets, tool_shed and all tools were on > another location, so I still have them. He deleted only galaxy directory. > Of course, I had some local tools an wrappers there, but at least I hope I > can still do something. > > > Thanks once again! > > Best, > > Marija > -- > *Von:* Nate Coraor > *Gesendet:* Donnerstag, 19. Oktober 2017 18:36 > *An:* Durdevic, Marija > *Cc:* galaxy-dev@lists.galaxyproject.org > *Betreff:* Re: [galaxy-dev] Urgent help needed > > Hi Marija, > > Wow, sorry to hear this. If the datasets themselves were removed, it's > unlikely there'd be a way to get them back. Some filesystems do have > undelete tools to attempt to recover data that has not yet been > overwritten. If you can stop all activity on that filesystem while > investigating and attempt to recover, this would likely increase the amount > of data you'd be able to recover. > > It would be possible to reconnect to the database assuming it was not > SQLite and also removed. Your existing backed up configs should do this > automatically. This would restore your users and their Galaxy > representations of things, such as histories, but without the actual data > in those histories. > > --nate > > On Thu, Oct 19, 2017 at 10:32 AM, Durdevic, Marija < > marija.durde...@medunigraz.at> wrote: > >> Dear developers, >> >> >> >> The colleague of mine mistakenly deleted my Galaxy installation (rm –rf >> *). Unfortunately there is no backup of complete installation. I have >> backup only configuration files. >> >> Is there any chance to fetch new Galaxy instance from git and to connect >> it to the old database? Or maybe any other suggestion what to do in such >> case? >> >> >> >> Many thanks in advance! >> >> >> >> Best, >> >> Marija >> >> >> >> *Mag. Marija Đurđević* >> >> Core Facility Computational Bioanalytics >> >> >> >> Medical University of Graz >> >> Center for Medical Research >> >> Stiftingtalstraße 24 >> <https://maps.google.com/?q=Stiftingtalstra%C3%9Fe+24&entry=gmail&source=g>, >> A-8010 Graz >> >> Austria >> >> >> >> Phone: +43 316/385-73024 <%2B43%20316%2F385-73024> >> >> Fax:+43 316/385-73009 >> >> >> >> Email: marija.durde...@medunigraz.at >> >> Email: marija.djurdje...@klinikum-graz.at >> >> >> >> Web: https://zmf.medunigraz.at/ >> >> >> >> >> >> ___ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> > > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Urgent help needed
What a tragedy! Be careful while use rm -rf. If happens,the right way is to shut down server and recover data from the disk. 发自我的 iPhone > 在 2017年10月20日，上午12:36，Nate Coraor 写道： > > Hi Marija, > > Wow, sorry to hear this. If the datasets themselves were removed, it's > unlikely there'd be a way to get them back. Some filesystems do have undelete > tools to attempt to recover data that has not yet been overwritten. If you > can stop all activity on that filesystem while investigating and attempt to > recover, this would likely increase the amount of data you'd be able to > recover. > > It would be possible to reconnect to the database assuming it was not SQLite > and also removed. Your existing backed up configs should do this > automatically. This would restore your users and their Galaxy representations > of things, such as histories, but without the actual data in those histories. > > --nate > >> On Thu, Oct 19, 2017 at 10:32 AM, Durdevic, Marija >> wrote: >> Dear developers, >> >> >> >> The colleague of mine mistakenly deleted my Galaxy installation (rm –rf *). >> Unfortunately there is no backup of complete installation. I have backup >> only configuration files. >> >> Is there any chance to fetch new Galaxy instance from git and to connect it >> to the old database? Or maybe any other suggestion what to do in such case? >> >> >> >> Many thanks in advance! >> >> >> >> Best, >> >> Marija >> >> >> >> Mag. Marija Đurđević >> >> Core Facility Computational Bioanalytics >> >> >> >> Medical University of Graz >> >> Center for Medical Research >> >> Stiftingtalstraße 24, A-8010 Graz >> >> Austria >> >> >> >> Phone: +43 316/385-73024 >> >> Fax:+43 316/385-73009 >> >> >> >> Email: marija.durde...@medunigraz.at >> >> Email: marija.djurdje...@klinikum-graz.at >> >> >> >> Web: https://zmf.medunigraz.at/ >> >> >> >> >> >> >> ___ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Urgent help needed
Hi Marija, Wow, sorry to hear this. If the datasets themselves were removed, it's unlikely there'd be a way to get them back. Some filesystems do have undelete tools to attempt to recover data that has not yet been overwritten. If you can stop all activity on that filesystem while investigating and attempt to recover, this would likely increase the amount of data you'd be able to recover. It would be possible to reconnect to the database assuming it was not SQLite and also removed. Your existing backed up configs should do this automatically. This would restore your users and their Galaxy representations of things, such as histories, but without the actual data in those histories. --nate On Thu, Oct 19, 2017 at 10:32 AM, Durdevic, Marija < marija.durde...@medunigraz.at> wrote: > Dear developers, > > > > The colleague of mine mistakenly deleted my Galaxy installation (rm –rf > *). Unfortunately there is no backup of complete installation. I have > backup only configuration files. > > Is there any chance to fetch new Galaxy instance from git and to connect > it to the old database? Or maybe any other suggestion what to do in such > case? > > > > Many thanks in advance! > > > > Best, > > Marija > > > > *Mag. Marija Đurđević* > > Core Facility Computational Bioanalytics > > > > Medical University of Graz > > Center for Medical Research > > Stiftingtalstraße 24, A-8010 Graz > > Austria > > > > Phone: +43 316/385-73024 <%2B43%20316%2F385-73024> > > Fax:+43 316/385-73009 > > > > Email: marija.durde...@medunigraz.at > > Email: marija.djurdje...@klinikum-graz.at > > > > Web: https://zmf.medunigraz.at/ > > > > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] URGENT HELP!
Not to worry, I was restarting another server. Its fixed now. Thanks
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: 29 October 2015 18:03
To: Ali Al-Shahib; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] URGENT HELP!
It looks like the Galaxy server was downgraded relative the database. Do you
know how this may have happened?
It also looks like this instance is probably quite a bit out of date, in any
event, so I'd be hesitant to give advice recommending a major upgrade given the
current state of things. I'd say you should really get in touch with the
Galaxy Admin prior to trying much.
Is using a cloud instance for the training an option?
On Thu, Oct 29, 2015 at 11:44 AM Ali Al-Shahib
mailto:ali.al-sha...@phe.gov.uk>> wrote:
Hi all
I am due to give galaxy training tomorrow and the Galaxy server has gone down.
Our galaxy admin is travelling and not responding and I appreciate a quick
response to this issue.
When I run galaxy_restart.sh I get the following error in web0.pid:
migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config:
{'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
lib/galaxy/model/migrate
galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg
successfully loaded for postgresql dialect
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 104,
in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '124' but this code expects version '115'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh upgrade'.
--
I did then try to do sh manage_db.sh downgrade 115 but I got this error:
Traceback (most recent call last):
File "./scripts/manage_db.py", line 62, in
main( repository=repo, url=db_url )
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py",
line 207, in main
ret = command_func(**kwargs)
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
line 202, in downgrade
return _migrate(url, repository, version, upgrade=False, err=err, **opts)
File "", line 2, in _migrate
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py",
line 159, in with_engine
return f(*a, **kw)
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
line 345, in _migrate
changeset = schema.changeset(version)
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py",
line 80, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
line 225, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
line 189, in version
return self.versions.version(*p, **k)
File
"/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py",
line 140, in version
return self.versions[VerNum(vernum)]
KeyError:
Any help asap will be greatly appreciated.
Ali
**
The information contained in the EMail and any attachments is confidential and
intended solely and for the attention and use of the named addressee(s). It may
not be disclosed to any other person without the express authority of Public
Health England, or the intended recipient, or both. If you are not the intended
recipient, you must not disclose, copy, distribute or retain this message or
any part of it. This footnote also confirms that this EMail has been swept for
computer viruses by Symantec.Cloud, but please re-sweep any attachments before
opening or saving. http://www.gov.uk/PHE
**
_
Re: [galaxy-dev] URGENT HELP!
It looks like the Galaxy server was downgraded relative the database. Do
you know how this may have happened?
It also looks like this instance is probably quite a bit out of date, in
any event, so I'd be hesitant to give advice recommending a major upgrade
given the current state of things. I'd say you should really get in touch
with the Galaxy Admin prior to trying much.
Is using a cloud instance for the training an option?
On Thu, Oct 29, 2015 at 11:44 AM Ali Al-Shahib
wrote:
> Hi all
>
> I am due to give galaxy training tomorrow and the Galaxy server has gone
> down. Our galaxy admin is travelling and not responding and I appreciate a
> quick response to this issue.
>
> When I run galaxy_restart.sh I get the following error in web0.pid:
>
> migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config:
> {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
> 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
>
> lib/galaxy/model/migrate
>
> galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg
> successfully loaded for postgresql dialect
>
> Traceback (most recent call last):
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
>
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
>
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
> ).get( '__file__', None ), self.config.database_engine_options, app=self )
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line
> 104, in create_or_verify_database
>
> % ( db_schema.version, migrate_repository.versions.latest, config_arg
> ) )
>
> Exception: Your database has version '124' but this code expects version
> '115'. Please backup your database and then migrate the schema by running
> 'sh manage_db.sh upgrade'.
>
>
> --
>
>
>
> I did then try to do sh manage_db.sh downgrade 115 but I got this error:
>
>
> Traceback (most recent call last):
>
> File "./scripts/manage_db.py", line 62, in
>
> main( repository=repo, url=db_url )
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py",
> line 207, in main
>
> ret = command_func(**kwargs)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
> line 202, in downgrade
>
> return _migrate(url, repository, version, upgrade=False, err=err,
> **opts)
>
> File "", line 2, in _migrate
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py",
> line 159, in with_engine
>
> return f(*a, **kw)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
> line 345, in _migrate
>
> changeset = schema.changeset(version)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py",
> line 80, in changeset
>
> changeset = self.repository.changeset(database, start_ver, version)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
> line 225, in changeset
>
> changes = [self.version(v).script(database, op) for v in versions]
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
> line 189, in version
>
> return self.versions.version(*p, **k)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py",
> line 140, in version
>
> return self.versions[VerNum(vernum)]
>
> KeyError:
>
>
> Any help asap will be greatly appreciated.
>
>
> Ali
>
> **
> The information contained in the EMail and any attachments is confidential
> and intended solely and for the attention and use of the named
> addressee(s). It may not be disclosed to any other person without the
> express authority of Public Health England, or the intended recipient, or
> both. If you are not the intended recipient, you must not disclose, copy,
> distribute or retain this message or any part of it. This footnote also
> confirms that this EMail has been swept for computer viruses by
> Symantec.Cloud, but please re-sweep any attachments before opening or
> saving. http://www.gov.uk/PHE
> **
> ___
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
