Genome assembly update: Amyelois transitella

[amcooksey]

Change old content

• [ ] back up and deprecate old Apollo2
• [ ] back up and deprecate old fasta files in BLAST
• [ ] back up and deprecate old fasta files in Hmmer

Add new content to i5k Workspace applications

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_032362555.1
• publication associated with assembly: TBD
• due date: Dec 20
• community contact: Raman Bansal

Tasks on Ceres:

• [x] 1. Create functional annotations (@amcooksey). https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#0-run-the-functional-annotation-pipeline
• [x] 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)
• [x] 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:

• [x] 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)
• [x] 3. Set up Tripal pages (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#6-set-up-tripal-pages)
• [x] 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)
• [x] 5. Set up data downloads (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#8-set-up-data-downloads)
• [x] 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)

[mpoelchau]

@amcooksey how are things going with this ticket? FYI it's an Ag100Pest update with a bunch of manual annotations...

[amcooksey]

looks like this one got lost in the shuffle. i will start the update this week.

[amcooksey]

updated apollo except for the manual annotations. liftoff has been run. the files are here: /app/data/other_species/amytra/ilAmyTran1.1/scaffold/analyses/manual-curation AND /project/nal_genomics/amanda.cooksey/manual_annotations_and_OGS/amytra/ilAmyTran1.1/scaffold/analyses/manual-curation

[amcooksey]

update is be complete now except for the manual annotations.

[mpoelchau]

@amcooksey the genome assembly page is actually a genome annotation page. This is why this assembly didn't show up in the genome list. I'm not sure there's a way to change the category - you may just have to create a new page and delete the old one. https://i5k.nal.usda.gov/bio_data/1394540

[amcooksey]

Made a new genome assembly page for Amyelois transitella genome assembly ilAmyTran1.1 (GCF_032362555.1) and deleted the old one.

[amcooksey]

manual annotations and metadata added. phase needs to be reconciled to the original liftoff phase for these two transcripts: 53e0df20-1b26-476c-9dbc-8607f56b034d 391515ed-e86a-437d-838d-1f012e209d5e