New organism: Anabrus simplex

[amcooksey]

See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)

• assembly accession number: GCF_040414725.1
• publication associated with assembly: No
• due date: 9/10/24
• community contact: Hojun Song, Texas A&M University

Tasks on Ceres:

• 1. Create functional annotations (@amcooksey). https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#0-run-the-functional-annotation-pipeline
• 2. Run the final_workflow.cwl component of the organism_onboarding pipeline (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#1-run-the-final_workflowcwl-component-of-the-organism_onboarding-pipeline-httpsgithubcomnal-i5korganism_onboarding)
• 3. Run RNA-Seq pipeline, steps 1 and 2 (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-RNA-Seq-data-to-an-i5k-Workspace-project-with-the-NAL_RNA_seq_annotation_pipeline)

Tasks on the NAL servers:

• 1. Move the final_workflow.cwl output from SCINet to apollo2-stage-node1 (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#3-move-the-final_workflowcwl-output-from-scinet-to-apollo2-stage-node1)
• 2. Apollo setup on the apollo2-stage-node1 and apollo2-node1 servers (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#4-apollo-setup-on-the-apollo2-stage-node1-and-apollo2-node1-servers)
• 3. Set up Tripal pages (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#6-set-up-tripal-pages)
• 4. Set up BLAST and HMMER (genomics-workspace) (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#7-set-up-blast-and-hmmer-genomics-workspace)
• 5. Set up data downloads (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#8-set-up-data-downloads)
• 6. Final Test List (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#10-final-test-list)
• 7. Advertising (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#10-advertising) (@mpoelchau)

[amcooksey]

load onto apollo (stage and prod). waiting for space on i5k servers to finish.

[amcooksey]

GCF_040417275.1 was suppressed: use GCF_040414725.1 instead

[amcooksey]

removed GCF_040417275.1 from apollo stage and prod

[amcooksey]

loaded the correct version into apollo stage and prod. waiting for space on i5k servers to finish.

[amcooksey]

data downloads complete on stage.
blast looks complete on stage but the genome isn't showing up in the list even though django says it should. I will wait to see if it appears. This species is kind of big and has been slow at every step.

[amcooksey]

finally added. everything is done except the genome blast. the genome is quite large but we should be able to add it to blast once we update to the newer blast version.

[mpoelchau]

thanks! I added the organism to the Apollo registration and the available genome browsers page, and published the tripal pages. Could you update the scaffold readme:
https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/anasim-%28Anabrus_simplex%29/Current%20Genome%20Assembly/1.Genome%20Assembly/ASM4041472v1/Scaffolds/readme.txt

I think after that I can advertise.

[amcooksey]

I updated the scaffold readme.

[mpoelchau]

Two more things:

• please add Maeva Techer and Jackson Linde as community contacts (from TAMU)
• could you add the following publication and associate it with the organism?

Hoang, T.; Foquet, B.; Rana, S.; Little, D.W.;Woller, D.A.; Sword, G.A.; Song, H. Development of RNAi Methods for the Mormon Cricket, Anabrus simplex (Orthoptera: Tettigoniidae). Insects 2022, 13, 739. https://doi.org/10.3390/insects13080739

[amcooksey]

added contacts and publication