Code

Release/113#951

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vinay-ebi merged 61 commits intomainEnsembl/ensembl-production:mainfrom release/113Ensembl/ensembl-production:release/113Copy head branch name to clipboardSep 3, 2024

+259-120

Commits

Commits on Apr 26, 2024

• Changed GENCODE Basic tag to 'gencode_basic' as per ENSINT-1885

  sgiorgetti

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Commits on Apr 29, 2024

• Minor fixes

  

  Tamara El Naboulsi

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• Missing semicolon

  

  Tamara El Naboulsi

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• Change glob parameters

  

  Tamara El Naboulsi

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  6b97c44

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• Remove debugging

  

  Tamara El Naboulsi

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  5d99a70

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• Fixes to prevent warnings

  

  Tamara El Naboulsi

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  577c6ba

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Commits on Apr 30, 2024

• Fix file paths

  

  Tamara El Naboulsi

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Commits on May 2, 2024

• Keep original files if no species file

  

  Tamara El Naboulsi

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  7fb4c04

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• Merge pull request #920 from TamaraNaboulsi/xref/new_python_pipeline

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  dpopleton

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Commits on May 10, 2024

• Updated HGNC custom download URL

  jmgonzmart

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  74296b6

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• Merge pull request #923 from jmgonzmart/release/113

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  vinay-ebi

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Commits on May 15, 2024

• moved ensembl/xrefs to ensembl/production/xrefs

  vinay-ebi

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  0c7c41f

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• Update xref.config

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  vinay-ebi

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Commits on May 16, 2024

• base load changed to ensembl.production.xrefs

  vinay-ebi

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• Merge pull request #925 from Ensembl/feature/nf_xref

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  vinay-ebi

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• Update requirements.txt

  JAlvarezJarreta

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Commits on May 20, 2024

• Updated default resources from 100mb to 1gb

  dpopleton

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• Merge pull request #928 from Ensembl/update/increase_rc

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  dpopleton

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• Merge pull request #921 from Ensembl/main

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  vinay-ebi

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• Merge pull request #926 from JAlvarezJarreta/patch-2

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  vinay-ebi

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Commits on May 23, 2024

• Updated JSON remodeler to stop Experimental push on scalar is now forbidden with new perl version

  dpopleton

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Commits on May 24, 2024

• Merge branch 'release/113' into merge_conflicts

  vinay-ebi

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  d1f6dbf

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• Merge pull request #930 from Ensembl/merge_conflicts

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  dpopleton

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  cdce7ed

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• Update xref_all_sources.json for RGD

  vinay-ebi

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  3290f21

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• Merge pull request #931 from Ensembl/xref_resource_update

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  vinay-ebi

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Commits on May 28, 2024

• Update tag names and info relating to gencode genesets

  nwillhoft

  committed
  975fa4a

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Commits on May 29, 2024

• Bugfix for files not being overwritten

  

  Tamara El Naboulsi

  committed
  95c1320

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• Merge pull request #929 from Ensembl/update/file_dump_perl_compatibility

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  dpopleton

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• Merge pull request #933 from TamaraNaboulsi/xref/bugfix

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  vinay-ebi

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Commits on Jun 4, 2024

• Fix for when no species file is found

  

  Tamara El Naboulsi

  committed
  3ad6a02

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• Merge pull request #934 from TamaraNaboulsi/xref/bugfix

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  vinay-ebi

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• Update ProteinFeatures analysis

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  vinay-ebi

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• Update ProteinFeatures_conf.pm

  vinay-ebi

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Commits on Jun 5, 2024

• Merge pull request #935 from Ensembl/bugifx/proteinfeatures

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  vinay-ebi

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Commits on Jun 19, 2024

• Update xref_sources.json

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  vinay-ebi

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  d283cf0

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• Update xref_all_sources.json

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  vinay-ebi

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  d74f87e

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• Merge pull request #938 from Ensembl/bugfix/update_xenbase

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  vinay-ebi

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Commits on Jun 20, 2024

• Fixed as per ENSPROD-9493

  sgiorgetti

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Commits on Jun 21, 2024

• Merge pull request #939 from Ensembl/fix113/alphafold-displaylabel

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  vinay-ebi

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Commits on Jun 24, 2024

• Fix use of keys on a scalar

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  jgtate

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Commits on Jun 26, 2024

• Fixes for 113 issues

  

  Tamara El Naboulsi

  committed
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Commits on Jun 27, 2024

• Merge pull request #941 from TamaraNaboulsi/xref/fixes

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  dpopleton

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Commits on Jul 1, 2024

• Merge pull request #940 from Ensembl/fix-keys-on-scalar

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  jgtate

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Commits on Jul 5, 2024

• Update SourceFactory.pm

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  vinay-ebi

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• Merge pull request #942 from Ensembl/bug/experimenta_scalar

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  vinay-ebi

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Commits on Jul 19, 2024

• Updated Base class with slurm default resource 1GB

  vinay-ebi

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• Update Typo GB

  vinay-ebi

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Commits on Jul 22, 2024

• Merge pull request #918 from Ensembl/fix113/gencode_basic

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  vinay-ebi

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• Merge pull request #932 from nwillhoft/fix113/update_tag_info

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  vinay-ebi

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• decompress upidump.lis.gz file before load to hive db

  vinay-ebi

  committed
  2b01517

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• delete the upidump file after loading into hive db

  vinay-ebi

  committed
  434e865

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• Update modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm

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  vinay-ebi

  and

  jgtate

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• Update modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm

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  vinay-ebi

  and

  jgtate

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• Merge pull request #943 from Ensembl/feature/slurm_resource

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  vinay-ebi

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Commits on Jul 23, 2024

• Merge pull request #946 from Ensembl/bugfix/pf_uniparc_gunzip

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  vinay-ebi

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Commits on Jul 25, 2024

• Include human and mouse symlinks

  pblins

  committed
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• include Mouse and Human symlinks

  

  Paulo Lins

  committed
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• include Mouse and Human symlinks

  

  Paulo Lins

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  ac6c741

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• Merge pull request #947 from pblins/include-human-and-mouse

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  vinay-ebi

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Commits on Aug 13, 2024

• Update ProteinFeatures_conf.pm

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  vinay-ebi

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• Merge pull request #949 from Ensembl/bugfix/pf_analysis_lc

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  vinay-ebi

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