ElasticSearch plugin with Apollo

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ElasticSearch plugin with Apollo

mictadlo
Hi,
I tried to install ElasticSearch plugin ( https://github.com/elsiklab/jbrowse_elasticsearch ) into Apollo. With the following steps:

  1. git clone https://github.com/GMOD/Apollo.git
  2. cd Apollo
  3. I added ElasticSearch to `cat docker-files/docker-apollo-config.groovy`

```
jbrowse {
    git {
        url = "https://github.com/GMOD/jbrowse"
        branch = "1.16.4-release"
    }
    plugins {
     ...
        ElasticSearch{
            git = 'https://github.com/elsiklab/jbrowse_elasticsearch'
            branch = 'master'
            alwaysRecheck = "true"
            alwaysPull = "true"
        }
    }
}

```
Next, I executed

```
docker build -t apollo .
docker run -it -v "$(pwd)"/mydata:/data -p 8888:8080 -p 8080:3000 apollo
```

  • http://localhost:8080/ does not work for elasticsearch
  • http://localhost:8888/ only Apollo works without elasticsearch
What did I miss?

Thank you in advance,

Michal




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Re: ElasticSearch plugin with Apollo

nathandunn

Just to follow-up, more details can be found here. https://github.com/GMOD/Apollo/issues/2190#issuecomment-515651504

On Saturday, July 27, 2019 at 5:11:06 PM UTC-7, Michał T. Lorenc wrote:
Hi,
I tried to install ElasticSearch plugin ( <a href="https://github.com/elsiklab/jbrowse_elasticsearch" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Felsiklab%2Fjbrowse_elasticsearch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGPXKlEQdamd4FogklfGsEhOsXdWA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Felsiklab%2Fjbrowse_elasticsearch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGPXKlEQdamd4FogklfGsEhOsXdWA&#39;;return true;">https://github.com/elsiklab/jbrowse_elasticsearch ) into Apollo. With the following steps:

  1. git clone <a href="https://github.com/GMOD/Apollo.git" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo.git\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGBotVSTTrq7U2KMMYx-7r3cKS3_g&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo.git\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGBotVSTTrq7U2KMMYx-7r3cKS3_g&#39;;return true;">https://github.com/GMOD/Apollo.git
  2. cd Apollo
  3. I added ElasticSearch to `cat docker-files/docker-apollo-config.groovy`

```
jbrowse {
    git {
        url = "<a href="https://github.com/GMOD/jbrowse" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFrXiFEyuJToF-kzkXnrrZSspAAA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEFrXiFEyuJToF-kzkXnrrZSspAAA&#39;;return true;">https://github.com/GMOD/jbrowse"
        branch = "1.16.4-release"
    }
    plugins {
     ...
        ElasticSearch{
            git = '<a href="https://github.com/elsiklab/jbrowse_elasticsearch" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Felsiklab%2Fjbrowse_elasticsearch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGPXKlEQdamd4FogklfGsEhOsXdWA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Felsiklab%2Fjbrowse_elasticsearch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGPXKlEQdamd4FogklfGsEhOsXdWA&#39;;return true;">https://github.com/elsiklab/jbrowse_elasticsearch'
            branch = 'master'
            alwaysRecheck = "true"
            alwaysPull = "true"
        }
    }
}

```
Next, I executed

```
docker build -t apollo .
docker run -it -v "$(pwd)"/mydata:/data -p 8888:8080 -p 8080:3000 apollo
```

  • <a href="http://localhost:8080/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHav3I9_aV-3Af2UKEFgwwK-QWYeQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8080%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHav3I9_aV-3Af2UKEFgwwK-QWYeQ&#39;;return true;">http://localhost:8080/ does not work for elasticsearch
  • <a href="http://localhost:8888/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8888%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG1IEUiEGhDshCILGpwhBi8h_PXIQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Flocalhost%3A8888%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG1IEUiEGhDshCILGpwhBi8h_PXIQ&#39;;return true;">http://localhost:8888/ only Apollo works without elasticsearch
What did I miss?

Thank you in advance,

Michal




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