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E104 EG51 Switch out of wbsp #46

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E104 EG51 Switch out of wbsp #46

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@pcm32 pcm32 commented Jun 24, 2021 •
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This PR contains changes for switching out of WBSP for celegans and smansoni. Should be rebased to develop once the E104 EG51 WBSP15 is merged.

TODO:

  • Check that all arrays are covered, removing if needed from backfill and checking whether E! has probes for those.

pcm32 and others added 30 commits April 21, 2021 10:14
@pcm32
canis_familiaris_ensgene_homolog removed from duck
79f2227
@suhaibMo @pcm32
removed cfamiliaris_homolog
8d24259
@suhaibMo @pcm32
added species beetle, cucumber and salmon
f8cfe7d
@a-solovyev12
Update release numbers- Ensembl 104 EnsemblGenomes 51 E!Protists 51 W…
05cfcf5 
…ormbase 15
@a-solovyev12
Update broken species config
4fe89da
@a-solovyev12
update broken species configs
ec8ec55
@a-solovyev12
Add new worm species
676327d
@pinin4fjords
Update some outdated genome builds in GTF URIs
0a4e307
@pinin4fjords
Merge branch 'feature/move_to_E104_EG51_WBPS15_EP51' of github.com:eb…
13a532a 
…i-gene-expression-group/atlas-annotations into feature/move_to_E104_EG51_WBPS15_EP51
@pcm32
Worms E104 (#45)
9a9118f 
* c_brenneri config file adjusted

* c_japonica changes

* c_briggsae

* Remove brenneri and japonica from WBSP

* c_remanei
@pinin4fjords
Fix for a couple of changed species names in Ensembl dirs
bf2731b
@pinin4fjords
Merge branch 'feature/move_to_E104_EG51_WBPS15_EP51' of github.com:eb…
c948078 
…i-gene-expression-group/atlas-annotations into feature/move_to_E104_EG51_WBPS15_EP51
@pcm32
Update gxa_reference for worms moved from WBSP to ENSEMBL (not celegans)
b91662f
@a-solovyev12
Fix broken species configs
4537d90
@a-solovyev12
Merge branch 'feature/move_to_E104_EG51_WBPS15_EP51' of github.com:eb…
3102daf 
…i-gene-expression-group/atlas-annotations into feature/move_to_E104_EG51_WBPS15_EP51
@a-solovyev12
Update broken species configs
47efdc8
@pcm32
Adds chenopodium quinoa
e00f547
@a-solovyev12
update the worm configs
2e65e4c
@a-solovyev12
update the worm configs
7f57581
@a-solovyev12
update the worm configs
3a9637c
@a-solovyev12
update quinoa
150f7c7
@a-solovyev12
update the worm configs
cb48278
@a-solovyev12
update the worm configs
b3e8465
@a-solovyev12
Update gxa_references
da84850
@a-solovyev12
Fix broken line
839dd11
@a-solovyev12
rename dog file
852cce5
@a-solovyev12
Revert "rename dog file"
350e8bf 
This reverts commit 852cce5.
@a-solovyev12
update dog config
b34afa2
@a-solovyev12
Update the moss entry species and mySQL names
9d03a7f
@a-solovyev12
Try species fix
9c430cd
a-solovyev12 and others added 27 commits May 27, 2021 16:29
@a-solovyev12
Fix sheep
4553a5e
@a-solovyev12
fix dog
8e6efd6
@a-solovyev12
fix dog
28c5adf
@a-solovyev12
fix sheep
2171aad
@a-solovyev12
remove faulty parameters for sheep
c65c094
@pcm32
Singularity based ensembl update
c56f5b6
@pcm32
Correct typo in directory
46d46ce
@pcm32
Typo on env var
09eb073
@pcm32
Missing command and made executable ensemblUpdate on singularity
ea20be2
@pcm32
realpath and exports for singularity
f5d9e62
@pcm32
Get plant ontology from purl URL and change encoding for po processing.
d3de5de
@pcm32
Let curl deal with redirects
35d0ba8
@pcm32
Use UTF-8 encoding for interpro
50e1125
@pcm32
Downgrade to ammonite 1.1.2 as used in the validators
a01fefc
@pcm32
Add and reorganise human probesets
db8d821
@pcm32
Additional human array
fa44807
@pcm32
Use gene id for symbol as symbol is not available for chenopodium
32dcca6 
Gene symbol not available in biomart
@pcm32
Musa acuminata use gene id for symbol as it is not available
8493d6c
@pcm32
Aspergillus use gene id for symbol as absent
ea937c2
@pcm32
Gene id for symbol on Zea mays
d8c07bf
@pcm32
Correct typo
9c14600
@pcm32
Salmon and anoplophora trail without chromosome filtering
4423d9e
@pcm32
Simply write to /tmp and clean up
0e4052f
@pcm32
Many missing species in species-properties.json
e246d18
@pcm32
Fix cucumis sativus FTP link
be8a571
@pcm32
Remove extra plants in ftp path
4a7a0d8
@pcm32
Move celegans and smansoni to E! genomes
00f76ca
@pcm32 pcm32 marked this pull request as draft June 24, 2021 08:18
@pcm32 pcm32 marked this pull request as ready for review October 21, 2021 07:45
@pcm32 pcm32 marked this pull request as draft October 21, 2021 07:45
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4 participants
@pcm32 @suhaibMo @a-solovyev12 @pinin4fjords