BLAT removing

Michał T. Lorenc

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Aug 19, 2022, 12:55:52 AM8/19/22

to apollo

Hi all,

Our IT department set up for us an Apollo instance. We want to remove BLAT from the search.

Where in the source code ( https://github.com/eresearchqut/Apollo ) can I find BLAT entries?

Thank you in advance,

Best wishes,

Michal

Nathan Dunn

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Aug 19, 2022, 1:02:08 PM8/19/22

to "Michał T. Lorenc", apollo

If the organism doesn’t have a BLAT DB defined, it shouldn’t show up.

https://github.com/eresearchqut/Apollo/blob/codebuild/src/gwt/org/bbop/apollo/gwt/client/MainPanel.java#L713

Worst case, if there is a bug, you can set it explicitly to false or you can comment out the component int he tab, but I would avoid that if possible: https://github.com/eresearchqut/Apollo/blob/codebuild/src/gwt/org/bbop/apollo/gwt/client/MainPanel.ui.xml#L188

Nathan

On Aug 18, 2022, at 9:55 PM, Michał T. Lorenc <m.t.l...@gmail.com> wrote:

Hi all,
Our IT department set up for us an Apollo instance. We want to remove BLAT from the search.

<image.png>
Where in the source code ( https://github.com/eresearchqut/Apollo ) can I find BLAT entries?

Thank you in advance,

Best wishes,

Michal

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Nathan Dunn

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Aug 21, 2022, 10:35:06 PM8/21/22

to "Michał T. Lorenc", apollo

That gets set in the Config.groovy, or what you override the config with:

sequence_search_tools = [
        blat_nuc : [
                search_exe  : "/usr/local/bin/blat",
                search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
                name        : "Blat nucleotide",
                params      : ""
        ],
        blat_prot: [
                search_exe  : "/usr/local/bin/blat",
                search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
                name        : "Blat protein",
                params      : ""
                //tmp_dir: "/opt/apollo/tmp" optional param
        ]
]

Pretty sure its just in order listed, so you can change it directly within the running apollo-config.groovy file it is deployed with (unless they edited the Config.groovy file directly).

Nathan

On Aug 21, 2022, at 5:11 PM, Michał T. Lorenc <m.t.l...@gmail.com> wrote:

Hi Nathan,
Thank you for your email. Is there a way to change the order of search options i.e. BLAST gets shown first?

<image.png>

Michał T. Lorenc

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Aug 22, 2022, 12:17:21 AM8/22/22

to Nathan Dunn, apollo

Hi Nathan,

Could you please show me where Config.groovy is located in https://github.com/eresearchqut/Apollo ?

Thank you in advance,

Best wishes,

Michal

Nathan Dunn

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Aug 22, 2022, 1:02:50 PM8/22/22

to "Michał T. Lorenc", apollo

You’ll have to talk to whoever set it up, but the instructions I described are below:

https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=blat#search-tools

Nathan

Michał T. Lorenc

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Aug 31, 2022, 9:20:02 PM8/31/22

to Nathan Dunn, apollo

Hi, It seems that they are using those files:

However, I can't find the BLAT settings to remove them from the Search menu or at least to change that Blast is first.

Best wishes,

Michal

Nathan Dunn

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Aug 31, 2022, 10:30:26 PM8/31/22

to "Michał T. Lorenc", apollo

I would rename the 2 keys so it overrides (i.e., blat_nuc and blat_prot instead of blast_nuc and blast_prot) and it should override without adding:

https://github.com/eresearchqut/Apollo/blob/codebuild/docker-files/docker-apollo-config.groovy#L144