Urgent help needed
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<tel:%2B43%20316%2F385-73024> Fax:+43 316/385-73009<tel:%2B43%20316%2F385-73009> Email: marija.durdevic@medunigraz.at<mailto:marija.durdevic@medunigraz.at> Email: marija.djurdjevic@klinikum-graz.at<mailto:marija.djurdjevic@klinikum-graz.at> Web: https://zmf.medunigraz.at/
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.durdevic@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.durdevic@medunigraz.at
Email: marija.djurdjevic@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/
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 <nate@bx.psu.edu> 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 <marija.durdevic@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
Fax:+43 316/385-73009
Email: marija.durdevic@medunigraz.at
Email: marija.djurdjevic@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/
?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 <nate@bx.psu.edu> 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.durdevic@medunigraz.at<mailto:marija.durdevic@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<tel:%2B43%20316%2F385-73024> Fax:+43 316/385-73009<tel:%2B43%20316%2F385-73009> Email: marija.durdevic@medunigraz.at<mailto:marija.durdevic@medunigraz.at> Email: marija.djurdjevic@klinikum-graz.at<mailto:marija.djurdjevic@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/
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.durdevic@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 <nate@bx.psu.edu> *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.durdevic@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.durdevic@medunigraz.at
Email: marija.djurdjevic@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/
?That's what I wanted to hear! Thanks a lot once again. Best, Marija ________________________________ Von: Nate Coraor <nate@bx.psu.edu> 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 <marija.durdevic@medunigraz.at<mailto:marija.durdevic@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 <nate@bx.psu.edu<mailto:nate@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 <marija.durdevic@medunigraz.at<mailto:marija.durdevic@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<tel:%2B43%20316%2F385-73024> Fax:+43 316/385-73009<tel:%2B43%20316%2F385-73009> Email: marija.durdevic@medunigraz.at<mailto:marija.durdevic@medunigraz.at> Email: marija.djurdjevic@klinikum-graz.at<mailto:marija.djurdjevic@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/
Hi all, I am facing some problem in building a galaxy tool from Rscript (using planemo). The error file is attached. Main error is: dyld: Library not loaded: @rpath/libintl.8.dylib I have tried suggestions from: https://github.com/tectonic-typesetting/tectonic/issues/40 Thank you, Deepak
Sorry, forgot to attach the error file! On Oct 20, 2017, at 12:21 PM, Deepak Tanwar <dktanwar@hotmail.com<mailto:dktanwar@hotmail.com>> wrote: Hi all, I am facing some problem in building a galaxy tool from Rscript (using planemo). The error file is attached. Main error is: dyld: Library not loaded: @rpath/libintl.8.dylib I have tried suggestions from: https://github.com/tectonic-typesetting/tectonic/issues/40 Thank you, Deepak ___________________________________________________________ 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/
participants (4)
-
Deepak Tanwar -
Durdevic, Marija -
Nate Coraor -
XiaoTao Jiang