Genome assembly update: Cephus cinctus

[mpoelchau]

OGS remapping (@mpoelchau)

• review OGS and remap if necessary
• remap 1 manual annotation

Change old content

• [x] back up and deprecate old Apollo2
• [x] back up and deprecate old fasta files in BLAST
• [x] 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_000341935.2
• publication associated with assembly: https://doi.org/10.1093/gbe/evy232
• due date: 9/5/2023
• community contact: i5k

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)
• [x] 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)
• [x] 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)

[mpoelchau]

@amcooksey I may need to add a track or 2 before you move from stage to prod.

[amcooksey]

The directories are all set up on stage.

[amcooksey]

I think I have finished. One issue--BLAST doesn't show genome fasta (shows other fasta seqs). This doesn't seem to be a permissions issue.