New organism: Venturia canescens

[mpoelchau]

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_019457755.1

• publication associated with assembly: none

• Due date: before October 8

• [x] 1. Run the final_workflow.cwl component of the organism_onboarding pipeline

• [x] 2. Add gene page linkouts from Apollo.

• [x] 2a. RNAseq https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-RNA-Seq-data-to-an-i5k-Workspace-project-with-the-NAL_RNA_seq_annotation_pipeline

• [x] 3. Move the final_workflow.cwl output from SCINet to apollo2-stage-node1.

• [x] 4. Apollo setup on the apollo2-stage-node1 server.

• [ ] 5. Ag Data Commons submission (Ignore this section for RefSeq data).

• [x] 6. Set up Tripal pages

• [x] 7. Set up BLAST and HMMER (genomics-workspace)

• [x] 8. Set up data downloads

• [x] 9. Functional annotation and RNA-Seq

• [x] 10. Final Test List

• [x] 11. Advertising

[suryasaha]

Add organism and fasta files

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addorganism Venturia canescens
Succeessfully add to database

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addblast Venturia canescens -t nucleotide Genome Assembly -f /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_genomic.fna -d 'Venturia canescens genome assembly, ASM1945775v1'

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addblast Venturia canescens -t nucleotide Transcript -f /usr/local/i5k/media/bl
ast/db/GCF_019457755.1_ASM1945775v1_rna_from_genomic.fna -d 'Venturia canescens NCBI Annotation Release 100, transcripts'

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addblast Venturia canescens -t peptide Protein -f /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_translated_cds.faa -d 'Venturia canescens NCBI Annotation Release 100, translated CDS'

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addblast Venturia canescens -t nucleotide Transcript -f /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_cds_from_genomic.fna -d 'Venturia canescens NCBI Annotation Release 100, CDS'

Make blast DBs and populate

(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_genomic.fna -m
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_genomic.fna -p

(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_rna_from_genomic.fna -m
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_rna_from_genomic.fna -p
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_translated_cds.faa -m
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_translated_cds.faa -p
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_cds_from_genomic.fna -m
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_utility /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_cds_from_genomic.fna -p

Make visible

(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_shown /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_genomic.fna --shown true
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_shown /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_rna_from_genomic.fna --shown true
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_shown /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_cds_from_genomic.fna --shown true
1 species finished
all done
(i5k) [i5k@i5k-stage-node1 ~]$ python  manage.py  blast_shown /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_translated_cds.faa --shown true

Add genome assembly fasta file to jbrowse

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addjbrowse /usr/local/i5k/media/blast/db/GCF_019457755.1_ASM1945775v1_genomic.fna https://apollo.nal.usda.gov/apollo/Venturia%20canescens/jbrowse/
JBrowseSetting Successfully Created.

Set up hmmer for peptide fasta fila:

(i5k) [i5k@i5k-stage-node1 ~]$ python manage.py addhmmer Venturia canescens -f /usr/local/i5k/media/blast/db/GCF_019457755.1_AS
M1945775v1_translated_cds.faa -d "Venturia canescens NCBI Annotation release 100, translated CDS"
Success

[mpoelchau]

Functional annotation links:

Do the following on BOTH i5k-stage and i5k

1. within the NCBI annotation subdirectory (e.g. /app/data/other_species/bracop/BU_Bcop_v1/scaffold/analyses/NCBI_Bradysia_coprophila_Annotation_Release_100/), create a new directory NCBI_Bradysia_coprophila_Annotation_Release_100_functional_annotation
2. Put the functional annotations there with the readme
3. Create a symbolic link to the new functional annotation directory from the data downloads directories (e.g. from /app/web/drupal7/data/Arthropoda/bracop-(Bradysia_coprophila)/BU_Bcop_v1/2.Official or Primary Gene Set/NCBI_Bradysia_coprophila_Annotation_Release_100)
4. Make sure that the new files and symlinks are 1) group-writable and 2) owned by the i5k group

[suryasaha]

No data-downloads directory on i5k-stage /app/web/drupal7/data/Arthropoda/ @mpoelchau

[suryasaha]

Tripal pages and data downloads including functional annotation look fine. Apollo looks good with RNAseq tracks. Genomics workspace results look fine but jbrowse linkouts are not working. Is this due to the path before the fasta?

[mpoelchau]

@suryasaha

• I've updated the documentation to include setting up the data downloads on stage, and have finished the process for Venturia.
• There was no jbrowse linkout on prod. I've added and tested it.
• For the organism page - we need to cite where the description is from, could you provide a URL?

[suryasaha]

Thanks! I will use the instructions for the tick.

I pulled the description from this paper as there was nothing on our usual sources https://www.sciencedirect.com/science/article/pii/B9780123848581000151