genomes of pecan and Chinese hickory

mestato commented 5 years ago

Publication and Data Information

https://academic.oup.com/gigascience/article/8/5/giz036/5484800

Additional Information

Checklist

See New Genome Documentation for detailed instructions.

[x] Create Organism
[x] Create Publication
[x] Create Reference Genome
[x] Create InterProScan Annotation
[x] Create BLAST Annotation
[x] Run Chado FASTA Loader for CDS
[x] Run Chado FASTA Loader for Polypeptides
[x] Publish Tripal content
[x] Create KEGG Annotation
[x] Run Chado KEGG Loader
[x] Run Chado BLAST XML results loader
[x] Run Chado InterProScan XML results loader
[x] Create Blast Database

patricksis commented 5 years ago

I was looking through the GeneBank to find these organism, couldn't find them. Maybe I'm looking in the wrong directory @mestato ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/

mestato commented 5 years ago

I was a reviewer of the paper so I know its available somewhere.... try this site: http://gigadb.org/dataset/100571

patricksis commented 5 years ago

Ah I should've checked Giga, thank you

patricksis commented 5 years ago

patricksis commented 5 years ago

patricksis commented 5 years ago

@almasaeed2010 got this error when trying to create the second genome Could not save the TripalEntity: Unable to write fields to Chado: Array ( [schema__publication] => Array ( [0] => Array ( [value] => 41 [chado-analysis_pub__analysis_pub_id] => [chado-analysis_pub__analysis_id] => [chado-analysis_pub__pub_id] => 41 [pub_title] => The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition [id:41] ) ) [local__source_data] => Array ( [0] => Array ( [value] => [chado-analysis__sourcename] => [chado-analysis__sourceversion] => __NULL__ [chado-analysis__sourceuri] => __NULL__ [source_data] => Array ( [sourcename] => [sourceversion] => [sourceuri] => ) ) ) [sio__annotation] => Array ( [0] => Array ( [value] => delete_me [chado-analysis_cvterm__analysis_cvterm_id] => [chado-analysis_cvterm__cvterm_id] => [chado-analysis_cvterm__analysis_id] => [cv_id] => 0 [cvterm_name] => [chado-analysis_cvterm__is_not] => [chado-analysis_cvterm__rank] => [chado-analysis_cvterm_is_not] => ) ) [sbo__database_cross_reference] => Array ( [0] => Array ( [value] => delete_me [chado-analysis_dbxref__analysis_dbxref_id] => [chado-analysis_dbxref__analysis_id] => [chado-analysis_dbxref__dbxref_id] => [db_id] => 0 [accession] => ) ) [field_number_of_scaffolds] => Array ( [0 Referesis_id] => [chado-analysisprop__value] => [chado-analysisprop__type_id] => [chado-analysisprop__rank] => ) ) [local__time_executed] => Array ( [0] => Array ( [value] => 2019-05-16 19:02:00 [show_todate] => 1 [timezone] => America/Halifax [offset] => -10800 [offset2] => -10800 [value2] => 2019-05-16 19:02:00 ) ) ) Cannot save entity

Maybe I should differentiate them somehow?

almasaeed2010 commented 5 years ago

Yeah they need to have a different version, program or type. The name alone doesn't count.

patricksis commented 5 years ago

For both of these organism, IPS results aren't showing up. Could someone take a look at this when they get a chance @mestato @almasaeed2010 ?

mestato commented 5 years ago

@almasaeed2010 needs to see the files, could you transfer them back over so he can take a look?

patricksis commented 5 years ago

All IPS files for Carya illinoinensis and Carya cathayensis have been added back to hardwoods. The paths are /var/www/html/sites/default/files/sequences/Carya_cathayensis/IPS/xmls and /var/www/html/sites/default/files/sequences/Carya_illinoinensis/IPS

almasaeed2010 commented 5 years ago

Thanks @patricksis I’ll look at them when I get a minute

almasaeed2010 commented 5 years ago

Files look fine. I submitted a new job without using any regular expressions to test.

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/790791

almasaeed2010 commented 5 years ago

The job worked. Probably was a simple mistake in the form somewhere.

patricksis commented 5 years ago

Thanks @almasaeed2010 I'll submit a new job for Carya illinoinensis

patricksis commented 5 years ago

Carya illinoinensis redo IPS: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/791195

patricksis commented 5 years ago

@cricha59 Can you look at these two organisms when you get the chance? IPS results might not show up, if they don't just reload the cache.

mestato commented 4 years ago

Reopening due to errors. On genome assembly page,

"-All gene models genome" should be "Genome scaffolds" (both species)
That link doesn't work and needs to be updated (cathayensis only)
the downloads need to use our typical HTML for downloadable files (both species)

For an example of how to structure download links please see https://hardwoodgenomics.org/Genome-assembly/2209433?tripal_pane=group_summary_tripalpane

patricksis commented 4 years ago

All links have been replaced and fixed with HTML format, as well as the labeling.

statonlab / hardwoods_site