Genome assembly update: Apis mellifera

[amcooksey]

OGS remapping

• [ ] request whole-genome alignment
• [ ] Set up data directories and get data
• [ ] run remap-gff3

Looks like there's an OGS add. We can use (and refer back to) HGD's version of this: https://data.elsiklab.missouri.edu/downloads/hgd/gene_gff3/ogs/Apis_mellifera_amel_OGSv3.2_liftover_Amel_HAv3.1.gff3.gz

page for the files: https://hymenoptera.elsiklab.missouri.edu/ogs_gff3_files

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_003254395.2
• publication associated with assembly: (https://pubmed.ncbi.nlm.nih.gov/30961563/)
• due date: 3/27
• community contact: Chris Elsik,elsikc@missouri.edu

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)
• [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. Add is_obsolete property to OLD genome assembly Tripal pages. See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/SOPs-for-I5k-Workspace-genome-project-updates#tripal-1
• [x] 5. 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] 6. Set up data downloads (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#8-set-up-data-downloads)
• [ ] 7. Final Test List (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#10-final-test-list)
• [ ] 8. Advertising (https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#10-advertising) (@mpoelchau)

[amcooksey]

https://data.elsiklab.missouri.edu/downloads/hgd/gene_gff3/ogs/Apis_mellifera_amel_OGSv3.2_liftover_Amel_HAv3.1.gff3.gz uses different chromosome names than the NCBI assembly/gff and doesn't display properly in JBrowse. Will have to do our own liftover.

[amcooksey]

update complete EXCEPT: unable to obsolete the old genome assembly drush command gives this error: Line 1 Analysis lookup by name (select) No Matching record in analysis where values:Array ( [name] => Apis mellifera genome assembly Amel_v4.5 (GCF_000002195.4) )

[site http://default] [TRIPAL ERROR] [TRIPAL_BULK] Line 1 Analysis lookup by name (select) No Matching record in analysis where values:Array( [name] => Apis mellifera genome assembly Amel_v4.5 (GCF_000002195.4))

[amcooksey]

organism page needs data downloads link. will have to revisit when pages are editable.

[amcooksey]

Apparently drupal/tripal trims extra whitespace. The name of the of the old assembly had an extra space in the database that didn't display on the site. Once I added the extra space to the name the obsolete process worked correctly.

[amcooksey]

fixed organism page. update complete.