how to add options in sequence search tool blat

[waterhouseBenth]

I have installed web based apollo in my local server. I found sequence search tool blat is embedded, could you please tell me how to add option "-binSize" in the blat? thanks

[waterhouseBenth]

I used gmod/stable version >docker pull gmod/apollo:stable

[waterhouseBenth]

I used gmod/stable version >docker pull gmod/apollo:stable to installed web based apollo in my local server. I found sequence search tool blat is embedded, could you please tell me how to add option "-tileSize" in the blat? thanks

[cmdcolin]

I haven't tested but you could try something like this

See docs here
https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=blat#main-configuration

    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
            ],
         blat_nuc_with_tilesize12 : [
                    search_exe  : "/usr/local/bin/blat",
                    search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
                    name        : "Blat tileSize 12 nucleotide",
                    params      : "-tileSize 12"
            ],

this hardcodes the parameter somewhat but hope that helps

[garrettjstevens]

To add on a bit, I think the syntax might need to be -tileSize=12 for the params.

Since you're using the Docker image, though, there isn't a way to change your config.groovy file and add this option. Your options are to run Apollo locally without Docker, or to create your own Docker image.

To create your own Docker image, clone the GitHub repository and make the changes you want to docker-files/docker-apollo-config.groovy. Then run docker build -t my_apollo_build . to build a new image. Then you can run your Docker container the same as you did before except replacing gmod/apollo:stable with my_apollo_build.