Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release/113 #951

Merged
merged 61 commits into from
Sep 3, 2024
Merged

Release/113 #951

merged 61 commits into from
Sep 3, 2024

Conversation

vinay-ebi
Copy link
Contributor

Merge release/113 changes to main to prepare release/114

sgiorgetti and others added 30 commits April 26, 2024 17:38
@sgiorgetti
Changed GENCODE Basic tag to 'gencode_basic' as per ENSINT-1885
d924e50
Minor fixes
a0b629a
Missing semicolon
ec58c92
Change glob parameters
6b97c44
Remove debugging
5d99a70
Fixes to prevent warnings
577c6ba
Fix file paths
a29d373
Keep original files if no species file
7fb4c04
@dpopleton
Merge pull request #920 from TamaraNaboulsi/xref/new_python_pipeline
c05a7d4 
Minor fixes
@jmgonzmart
Updated HGNC custom download URL
74296b6
@vinay-ebi
Merge pull request #923 from jmgonzmart/release/113
66f0ff4 
Updated HGNC custom download URL
@vinay-ebi
moved ensembl/xrefs to ensembl/production/xrefs
0c7c41f
@vinay-ebi
Update xref.config
0393357 
add memory 4gg to slurm profile
@vinay-ebi
base load changed to ensembl.production.xrefs
4391762
@vinay-ebi
Merge pull request #925 from Ensembl/feature/nf_xref
fde8b7b 
moved ensembl/xrefs to ensembl/production/xrefs
@JAlvarezJarreta
Update requirements.txt
6f63ae1
@dpopleton
Updated default resources from 100mb to 1gb
15b4ead
@dpopleton
Merge pull request #928 from Ensembl/update/increase_rc
d9ac953 
Updated default resources from 100mb to 1gb
@vinay-ebi
Merge pull request #921 from Ensembl/main
2c33d61 
Main
@vinay-ebi
Merge pull request #926 from JAlvarezJarreta/patch-2
7859b31 
Update requirements.txt
@dpopleton
Updated JSON remodeler to stop Experimental push on scalar is now for…
2021302 
…bidden with new perl version
@vinay-ebi
Merge branch 'release/113' into merge_conflicts
d1f6dbf
@dpopleton
Merge pull request #930 from Ensembl/merge_conflicts
cdce7ed 
Merging Slurm partition to 113
@vinay-ebi
Update xref_all_sources.json for RGD
3290f21
@vinay-ebi
Merge pull request #931 from Ensembl/xref_resource_update
808b346 
Update xref_all_sources.json for RGD
@nwillhoft
Update tag names and info relating to gencode genesets
975fa4a
Bugfix for files not being overwritten
95c1320
@dpopleton
Merge pull request #929 from Ensembl/update/file_dump_perl_compatibility
ba155dc 
Updated JSON remodeler to stop Experimental push on scalar is now for…
@vinay-ebi
Merge pull request #933 from TamaraNaboulsi/xref/bugfix
1c15ef9 
Xref bugfix
Fix for when no species file is found
3ad6a02
sgiorgetti and others added 24 commits June 20, 2024 13:36
@sgiorgetti
Fixed as per ENSPROD-9493
b2da23c
@vinay-ebi
Merge pull request #939 from Ensembl/fix113/alphafold-displaylabel
7463aca 
Fixed  as per ENSPROD-9493
@jgtate
Fix use of keys on a scalar
7e4aca5 
Change the use of an experimental, now removed, feature that allowed a hashref scalar to be used in place of a hash.
Fixes for 113 issues
a3ff2b4
@dpopleton
Merge pull request #941 from TamaraNaboulsi/xref/fixes
39c3a57 
Xref fixes
@jgtate
Merge pull request #940 from Ensembl/fix-keys-on-scalar
6549a72 
Fix use of keys on a scalar
@vinay-ebi
Update SourceFactory.pm
ee5da99 
Fix for Experimental keys on a scalar is now forbidden
@vinay-ebi
Merge pull request #942 from Ensembl/bug/experimenta_scalar
2976823 
Update SourceFactory.pm
@vinay-ebi
Updated Base class with slurm default resource 1GB
d1ce293
@vinay-ebi
Update Typo GB
772caf1
@vinay-ebi
Merge pull request #918 from Ensembl/fix113/gencode_basic
ce884ca 
Changed GENCODE Basic tag to 'gencode_basic'
@vinay-ebi
Merge pull request #932 from nwillhoft/fix113/update_tag_info
14500c9 
Update GENCODE tag info in header
@vinay-ebi
decompress upidump.lis.gz file before load to hive db
2b01517
@vinay-ebi
delete the upidump file after loading into hive db
434e865
@vinay-ebi @jgtate
Update modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUn…
693c899 
…iParc.pm

Co-authored-by: John Tate <[email protected]>
@vinay-ebi @jgtate
Update modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUn…
51cc0c3 
…iParc.pm

Co-authored-by: John Tate <[email protected]>
@vinay-ebi
Merge pull request #943 from Ensembl/feature/slurm_resource
7cbce1e 
Feature/slurm_resource
@vinay-ebi
Merge pull request #946 from Ensembl/bugfix/pf_uniparc_gunzip
515063a 
Bugfix/pf uniparc gunzip
@pblins
Include human and mouse symlinks
0eae3f6
include Mouse and Human symlinks
3542ca1
include Mouse and Human symlinks
ac6c741
@vinay-ebi
Merge pull request #947 from pblins/include-human-and-mouse
8380bd1 
Include human and mouse in the Regulation FTP symlink approach.
@vinay-ebi
Update ProteinFeatures_conf.pm
bbc1362 
Update the Protein feature analysis logic name to lowercase
@vinay-ebi
Merge pull request #949 from Ensembl/bugfix/pf_analysis_lc
d26c79e 
Update ProteinFeatures_conf.pm
@vinay-ebi vinay-ebi requested review from jgtate and dpopleton August 28, 2024 15:36
@vinay-ebi vinay-ebi requested a review from jgtate September 3, 2024 14:01
@vinay-ebi vinay-ebi merged commit 3045fbb into main Sep 3, 2024
2 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@TamaraNaboulsi TamaraNaboulsi TamaraNaboulsi left review comments

@jgtate jgtate jgtate approved these changes

@dpopleton dpopleton Awaiting requested review from dpopleton

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
9 participants
@vinay-ebi @jgtate @TamaraNaboulsi @sgiorgetti @dpopleton @jmgonzmart @JAlvarezJarreta @nwillhoft @pblins