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Add ability for indexed sequence file to be uploaded and used in an assembly #432

Merged
merged 29 commits into from
Sep 21, 2024
Merged

Add ability for indexed sequence file to be uploaded and used in an assembly #432

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7ad394b
Start implementing file upload|download|get
dariober Jul 8, 2024
ef4ec71
Add delete command and various small edits
dariober Jul 9, 2024
07b0a09
Add FileCommand handling file operations
dariober Jul 10, 2024
4ead5e0
Handle default profile via undefined
dariober Jul 10, 2024
7112709
Download file as stream
dariober Jul 11, 2024
2f34028
Handling of gzip input and bgzip'd & indexed fasta
dariober Jul 22, 2024
7b3255e
Fix linter
dariober Jul 22, 2024
e8a1919
Formatting
garrettjstevens Aug 30, 2024
16aebbb
Add description for file CLI topic
garrettjstevens Aug 30, 2024
ae152ca
Deduplicate sequence fetching code
garrettjstevens Aug 30, 2024
57d553e
Reference File schema from Assembly schema
garrettjstevens Aug 30, 2024
fc363d9
Rename commands
dariober Sep 4, 2024
63f2615
Remove -i option since file is positional
dariober Sep 4, 2024
b149a7f
Rename option --no-db and some other fixes
dariober Sep 4, 2024
48d2115
Add additional type and make input arg required
dariober Sep 4, 2024
f4b6887
Tmp commit
dariober Sep 6, 2024
9467881
fix app start issue
shashankbrgowda Sep 12, 2024
dc6dd33
fix lint
shashankbrgowda Sep 12, 2024
6865ff8
Tmp commit addressing https://github.com/GMOD/Apollo3/pull/432
dariober Sep 17, 2024
e1c8777
Tmp commit
dariober Sep 17, 2024
25bdefc
This should address comments in https://github.com/GMOD/Apollo3/pull/432
dariober Sep 18, 2024
860575a
Temp commit to fix buffer
dariober Sep 18, 2024
60ce5b2
Fix filehandle type
garrettjstevens Sep 18, 2024
12c83f1
Use files service to get filehandles
garrettjstevens Sep 18, 2024
3526bb8
Fix fileId vs fileIds and other issues for https://github.com/GMOD/Ap…
dariober Sep 19, 2024
1302ce4
Allow fasta input to be gzip
dariober Sep 20, 2024
9d149dc
Fixes after rebase
garrettjstevens Sep 20, 2024
db455a3
Move LocalFileGzip to collab server package
garrettjstevens Sep 20, 2024
14a2ada
Match selector to other updated tests
garrettjstevens Sep 20, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/reload_demo_data.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -84,8 +84,8 @@ jobs:

apollo assembly get | apollo assembly delete -v -a -

apollo assembly add-fasta -i $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f
apollo assembly add-fasta -i $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f
apollo assembly add-from-fasta $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f
apollo assembly add-from-fasta $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f

apollo feature import -i $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3 -a schistosoma_haematobium -d
apollo feature import -i $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3 -a schistosoma_mansoni -d
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8 changes: 4 additions & 4 deletions docs/automated_setup.md
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Expand Up @@ -22,9 +22,9 @@ wget https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/speci

gunzip *.gz

apollo assembly add-fasta ${P} -i schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f
apollo assembly add-fasta ${P} -i schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f
apollo assembly add-from-fasta ${P} schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f
apollo assembly add-from-fasta ${P} schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f

apollo feature import ${P} -i schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3 -a schistosoma_haematobium -d
apollo feature import ${P} -i schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3 -a schistosoma_mansoni -d
apollo feature import ${P} schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3 -a schistosoma_haematobium -d
apollo feature import ${P} schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3 -a schistosoma_mansoni -d
```
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