Best Way to "clone" My Local Galaxy instance

Question: Best Way to "clone" My Local Galaxy instance

3.4 years ago by

France

Hi guys,

I have a local instance of development for galaxy, and I would like to know, what is the best way to clone this local instance?

I mean, here I don't care about the DB or about existing data. I would like to keep all the tools/development I made on my local instance to launch a new production instance.

Is it ok to : 1- copy the whole galaxy folder, 2- Create a new postgresql DB, 3- modify the galaxy.ini for this new DB ?

In this case I wonder how I could properly delete all the existing data in this copy instance before using it (since the new DB would not include these dataset)

Is it a better choice to clone from galaxy website, and then to replace the tools folders and the configurations files?

Thank you for your guidance

Christ

clone local instance • 1.0k views

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modified 3.4 years ago • written 3.4 years ago by christophe.habib • 340

3.4 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Hi Christ

For a simple installation, it is ok to to a one to one copy of the complete galaxy folder, with the exception of the "database/files/' folder.

However, it depends where you have got the tools from. Have you used the toolshed to get the tools or have you added them all manually? Have you run an galaxy code update and thereby have migrated tools? All this might cause troubles when you start with a new (empty) PostgreSQL database.

Why not copy everything (including making a copy of your PostgreSQL database). And then delete all your existing datasets and histories once the new server is upa and running.

Hope this helps, Hans-Rudolf

ADD COMMENT • link written 3.4 years ago by Hotz, Hans-Rudolf • 1.8k

3.4 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hi Hans-Rudolf,

The tools mainly come from the toolshed. The tools that are not from the toolshed are located in a folder outside the galaxy folder. So I just have to add the tool conf file of our tools in the galaxy.ini for these tools.

However I don't understand what issue the galaxy code update could do with the PostgreSQL database. Could you explain it please (maybe a simple example would help me)? I would like to avoid misunderstanding.

This one to one copy seems the easiest and the fastest way to clone my instance here. But for future purpose I think I have to consider the possibility of copying everything.

Thank you for your help and your answers.

Christ

ADD COMMENT • link written 3.4 years ago by christophe.habib • 340

Depending on which code update you have done, some tools (which used to be part of the distribution) moved to the toolshed and this is stored in the "migrate_tools" table. I don't know how an empty PostgreSQL database will handle this. Maybe it populates itself with the information in lib/tool_shed/galaxy_install/migrate/versions/ This needs to be tested

ADD REPLY • link written 3.4 years ago by Hotz, Hans-Rudolf • 1.8k

3.4 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hi Hans-Rudolf,

I tried to clone my instance. To do so I copied the whole folder Galaxy, I deleted the database/files/* and then I defined a new database. It worked really well since I found all the reference genomes and the tools I installed in the previous instance are available (and working).

Unfortunately I just found out that something is lacking. When I click on "Manage Installed tool shed repositories" in the admin panel, there is no tools here. It is really troublesome because I need to manage this tools to stay up-to-date.

Do you have any idea about the way to retrieve all the tools previously installed from tool shed?

Thank you for your help

Christ

ADD COMMENT • link written 3.4 years ago by christophe.habib • 340

Well, that's why I did suggest as a safer option to "copy everything (including making a copy of your PostgreSQL database). And then delete all your existing datasets and histories once the new server is up and running"

Nevertheless, in order to rescue your new set-up, have a look at the "tool_dependency", " tool_shed_repository", "tool_version", and "tool_version_association" tables, and copare their contanst bewteen the old and the new database

Hans-Rudolf

ADD REPLY • link written 3.4 years ago by Hotz, Hans-Rudolf • 1.8k

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