Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
On 05/03/2012 08:29 PM, Robert Chase wrote: Hello, We have an existing galaxy instance that uses MySQL, has workflows and data libraries and countless changes to the source code and tools. We would like to save the database, workflows and data libraries but bring all the sourcecode up to date with the standard galaxy code. Because over 3000 of our files have been changed, we do not believe that we can realistically run hg update and then hg merge. We have built a test instance of galaxy that runs on a different virtual machine. One thought is to clone it, migrate all the datasets to it and then use the clone as the new production instance. One specific piece of information would be very helpful. Can we just copy the ~/data files to the test instance and have galaxy recognize them or is there metadata stored in the database? Hi Rob 3000 You need a copy of your MySQL database for your new test instance of galaxy to connect to. This should get you going initially. Most likely, you will then stumble across a few problems: - you need to sync ~/galaxy_dist/tool-data/shared/ - you need to check the data libraries: are they copies or sym-links - you need to decide how many of you changes to the tools you want to port to the new server. In an ideal world you would need all in order to maintain the reproducibility...this might be tricky, especially if you have defined your own data types. In this case a simple copy of the 'tools/' directory and the 'tool_conf.xml' is not sufficient anymore - an more... Nevertheless, you said you made more than 3000 changes to code and tools, so I guess, you are very proficient with the inner works of Galaxy. Hence, I see no problem, why you should not be successful. Regards, Hans -Rob On Wed, Mar 28, 2012 at 10:16 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Rob I don't know what exactly you mean by new server. Assuming you are just talking about different hardware: Have you considered moving 'everything' to the new server? ie copying the Galaxy directory tree (especially make sure you copy ~/database/ ) and connect to the same PostgreSQL (or MySQL) database. If you want, I can give you more details how we successfully changed the hardware of our server last year Regards, Hans On 03/28/2012 03:31 PM, Robert Chase wrote: Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab _ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hello, We have an existing galaxy instance that uses MySQL, has workflows and data libraries and countless changes to the source code and tools. We would like to save the database, workflows and data libraries but bring all the sourcecode up to date with the standard galaxy code. Because over 3000 of our files have been changed, we do not believe that we can realistically run hg update and then hg merge. We have built a test instance of galaxy that runs on a different virtual machine. One thought is to clone it, migrate all the datasets to it and then use the clone as the new production instance. One specific piece of information would be very helpful. Can we just copy the ~/data files to the test instance and have galaxy recognize them or is there metadata stored in the database? -Rob On Wed, Mar 28, 2012 at 10:16 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Rob I don't know what exactly you mean by new server. Assuming you are just talking about different hardware: Have you considered moving 'everything' to the new server? ie copying the Galaxy directory tree (especially make sure you copy ~/database/ ) and connect to the same PostgreSQL (or MySQL) database. If you want, I can give you more details how we successfully changed the hardware of our server last year Regards, Hans On 03/28/2012 03:31 PM, Robert Chase wrote: Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab __**__**_ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hi Rob I don't know what exactly you mean by new server. Assuming you are just talking about different hardware: Have you considered moving 'everything' to the new server? ie copying the Galaxy directory tree (especially make sure you copy ~/database/ ) and connect to the same PostgreSQL (or MySQL) database. If you want, I can give you more details how we successfully changed the hardware of our server last year Regards, Hans On 03/28/2012 03:31 PM, Robert Chase wrote: Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab _ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab __**_ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab ___ 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: http://lists.bx.psu.edu/
