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Insyght, a conserved synteny - homolog browser
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Insyght, a conserved synteny - homolog browser
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8732
Amélioration
Closed
Normal
Pipeline rev 471 ; improve the accessibility of the VM by simplifying the pipeline into 1 master script (keeping error handling proper)
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:09 PM
8731
Bug
Closed
Normal
Pipeline rev 471 ; check_for_element_types_and_reorganize_elements_into_organisms.pl want to update already updated element type from previous run
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:08 PM
8730
Bug
Closed
Normal
Pipeline rev 471 ; ObjectElement.pm -> setaccession -> deal with multiple digit in accnum name, do not file prefix and postfix
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:07 PM
8729
Amélioration
Closed
Normal
Pipeline rev 471 ; check_db_consistency.pl : test that element lenght = sequence lenght
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:07 PM
8728
Amélioration
Closed
Normal
Pipeline rev 471 ; check_db_consistency.pl : test that genes.residues = micado.prot.feat.residues
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:06 PM
8727
Amélioration
Closed
Normal
Pipeline rev 471 ; script download_from_ncbi.pl : add the option -restrict_to_list_taxon_id_and_subnodes
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:05 PM
8726
Feature
Closed
Normal
Pipeline rev 471 ; organize molecules into living organisms using assembly info
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:01 PM
8725
Feature
Closed
Normal
adapt to database schema rev 2: additional links and info from ncbi, add columns for convenience when querying the database (avoid cross tables querying)
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:00 PM
8724
Amélioration
Closed
Normal
Pipeline rev 471 ; Task_add_entry (insert of primary data) : Make the script more resilient to errors and re-run, faster (generator and integrator)
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:47 AM
8723
Amélioration
Closed
Normal
Pipeline rev 471 ; fill_gene_entry.pl : generate data for table gene directly instead of after schema micado is filled w/ data
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:46 AM
8722
Amélioration
Closed
Normal
Pipeline rev 471 ; fill_gene_entry.pl : infer correct type directly here instead of subsequent script
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:45 AM
8721
Feature
Closed
Normal
Pipeline rev 471 ; add bdlink info on ncbi assembly id and accession, etc... for the table organisms (trough element accnum)
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:44 AM
8719
Amélioration
Closed
Normal
Pipeline rev 471 ; improved analyse_stats_db.pl
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:34 AM
8718
Feature
Closed
Normal
Pipeline rev 471 ; created script download_genome_files_from_ncbi.pl
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:33 AM
8717
Amélioration
Closed
Normal
Pipeline rev 471 ; fill_gene_entry.pl : add Locus_tag directly in table genes
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:30 AM
8716
Amélioration
Closed
Normal
Pipeline rev 471 ; Task_add_entry : cleaner option -GENOME_FILES_FORMAT
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:25 AM
8715
Amélioration
Closed
Normal
Pipeline rev 471 ; Task_add_entry : added option -SKIP_NEIGHBOR_INFO as this info is not useful
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:23 AM
8714
Bug
Closed
Normal
Navigation jumps when moving with >> or << in ortholog table or genomic organisation
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:58 AM
8713
Bug
Closed
Normal
Compared organisms not sorted correctly for scope Whole organism
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:58 AM
8712
Bug
Closed
Normal
Synteny symbol not displaying correct number of pairs, it was missing gene mismatch and insertion
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:57 AM
8711
Bug
Closed
Normal
When transfering q genes from synteny to ortholog table view, s_insertion genes were transeferd as well
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:57 AM
8710
Bug
Closed
Normal
Error when the database was empty. Redirect user to use the guide to add data or check out http://genome.jouy.inra.fr/Insyght/ to test functionalities
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:57 AM
8709
Amélioration
Closed
Normal
Modified user interface to deal with database changes in schema: removal of elements.description (-> sequences.definition), elements.date_seq (-> sequences.date_seq), elements.version (-> sequences.version), genes.residue (-> prot_feat.proteine)
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:56 AM
8708
Bug
Closed
Normal
Fixed functionality to send email via smtp inra to report uncaught exception
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:55 AM
8707
Bug
Closed
Normal
Fixed examples taxon ids for release Archaea
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:55 AM
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