Urgent help needed

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Urgent help needed

Durdevic, Marija

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: <a href="tel:%2B43%20316%2F385-73024" target="_blank">+43 316/385-73024

Fax:<a href="tel:%2B43%20316%2F385-73009" target="_blank">+43 316/385-73009

 

Email: [hidden email]

Email: [hidden email]

 

Web: https://zmf.medunigraz.at/

 

 


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Re: Urgent help needed

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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: <a href="tel:%2B43%20316%2F385-73024" target="_blank">+43 316/385-73024

Fax:<a href="tel:%2B43%20316%2F385-73009" target="_blank">+43 316/385-73009

 

Email: [hidden email]

Email: [hidden email]

 

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/


___________________________________________________________
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Re: Urgent help needed

XiaoTao Jiang
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 <[hidden email]> 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 <[hidden email]> 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: <a href="tel:%2B43%20316%2F385-73024" target="_blank">+43 316/385-73024

Fax:<a href="tel:%2B43%20316%2F385-73009" target="_blank">+43 316/385-73009

 

Email: [hidden email]

Email: [hidden email]

 

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:
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___________________________________________________________
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Re: Urgent help needed

Durdevic, Marija
In reply to this post by Nate Coraor (nate@bx.psu.edu)

​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 <[hidden email]>
Gesendet: Donnerstag, 19. Oktober 2017 18:36
An: Durdevic, Marija
Cc: [hidden email]
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 <[hidden email]> 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: <a href="tel:%2B43%20316%2F385-73024" target="_blank">+43 316/385-73024

Fax:<a href="tel:%2B43%20316%2F385-73009" target="_blank">+43 316/385-73009

 

Email: [hidden email]

Email: [hidden email]

 

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/


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Urgent help needed

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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 <[hidden email]>
Gesendet: Donnerstag, 19. Oktober 2017 18:36
An: Durdevic, Marija
Cc: [hidden email]
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 <[hidden email]> 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: <a href="tel:%2B43%20316%2F385-73024" target="_blank">+43 316/385-73024

Fax:<a href="tel:%2B43%20316%2F385-73009" target="_blank">+43 316/385-73009

 

Email: [hidden email]

Email: [hidden email]

 

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:
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Re: Urgent help needed

Durdevic, Marija

​That's what I wanted to hear! Thanks a lot once again.


Best,

Marija


Von: Nate Coraor <[hidden email]>
Gesendet: Donnerstag, 19. Oktober 2017 18:59
An: Durdevic, Marija
Cc: [hidden email]
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 <[hidden email]> 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 <[hidden email]>
Gesendet: Donnerstag, 19. Oktober 2017 18:36
An: Durdevic, Marija
Cc: [hidden email]
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 <[hidden email]> 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: <a href="tel:%2B43%20316%2F385-73024" target="_blank">+43 316/385-73024

Fax:<a href="tel:%2B43%20316%2F385-73009" target="_blank">+43 316/385-73009

 

Email: [hidden email]

Email: [hidden email]

 

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/



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Job error

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

Thank you,
Deepak



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Re: Job error

Deepak Tanwar
Sorry, forgot to attach the error file!




On Oct 20, 2017, at 12:21 PM, Deepak Tanwar <[hidden email]> 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

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:
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___________________________________________________________
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