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GMOD / docker-apollo

:whale: Apollo 2.X Docker Image
GNU General Public License v3.0
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Apollo docker running... but now ? #28

Closed agroppi closed 5 years ago

agroppi commented 6 years ago

Hi,

After many unsuccesfull try to install Apollo, I shifted to the docker version : But, I realise that it's impossible to add data after that. I have to generate the data (ref genome, and all gff file) inside a jbrowse-data directory and after that run apollo-docker Am I right ? But in this case, where can I find the scripts described here : https://genomearchitect.readthedocs.io/en/latest/Data_loading.html#data-generation-pipeline

Thanks

nathandunn commented 6 years ago

After many unsuccesfull try to install Apollo

What were the errors / what was your system?

I have to generate the data (ref genome, and all gff file) inside a jbrowse-data directory and after that run apollo-docker Am I right ?

Yes. You have to mount it with the -v options.

But in this case, where can I find the scripts described here : https://genomearchitect.readthedocs.io/en/latest/Data_loading.html#data-generation-pipeline

Those scripts are within the JBrowse directory, either in jbrowse/bin or bin

Conversely, if you use indexed fasta and tabix gff3, you can just manually edit the trackList.json / tracks.conf

Examples of both are in here:

http://jbrowse.org/docs/tutorial.html

agroppi commented 6 years ago

After many unsuccesfull try to install Apollo

What were the errors / what was your system?

It seems that the problem is linked to mysql (MariaDB). When I omit to install MariaDB, the the local instance ./apollo run-local is working

I'm working on CentOS7

I have to generate the data (ref genome, and all gff file) inside a jbrowse-data directory and after that run apollo-docker Am I right ?

Yes. You have to mount it with the -v options.

But in this case, where can I find the scripts described here : https://genomearchitect.readthedocs.io/en/latest/Data_loading.html#data-generation-pipeline

Those scripts are within the JBrowse directory, either in jbrowse/bin or bin

OK but, inside the docker ... I will grep them from the github and execute outside the container

Conversely, if you use indexed fasta and tabix gff3, you can just manually edit the trackList.json / tracks.conf

Examples of both are in here:

http://jbrowse.org/docs/tutorial.html

Thanks :)