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"alignment/primary/reptiles/GCF_030035675.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/reptiles/GCF_030035675.1.repeatModeler.families.fa.gz" + }, + "GCF_030867095.1": { + "2bit": "alignment/primary/reptiles/GCF_030867095.1.2bit", + "fa": "alignment/primary/reptiles/GCF_030867095.1.fa.gz" + }, + "GCF_031021105.1": { + "2bit": "alignment/primary/reptiles/GCF_031021105.1.2bit", + "fa": "alignment/primary/reptiles/GCF_031021105.1.fa.gz" + }, + "GCF_035149785.1": { + "2bit": "alignment/primary/reptiles/GCF_035149785.1.2bit", + "fa": "alignment/primary/reptiles/GCF_035149785.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/reptiles/GCF_035149785.1.repeatModeler.families.fa.gz" + }, + "GCF_037176765.1": { + "2bit": "alignment/primary/reptiles/GCF_037176765.1.2bit", + "fa": "alignment/primary/reptiles/GCF_037176765.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/reptiles/GCF_037176765.1.repeatModeler.families.fa.gz" + }, + "GCF_963506605.1": { + "2bit": "alignment/primary/reptiles/GCF_963506605.1.2bit", + "fa": "alignment/primary/reptiles/GCF_963506605.1.fa.gz" + }, + "GCF_009764475.1": { + "2bit": "alignment/primary/sharks/GCF_009764475.1.2bit", + "fa": "alignment/primary/sharks/GCF_009764475.1.fa.gz" + }, + "GCF_010909765.2": { + "2bit": "alignment/primary/sharks/GCF_010909765.2.2bit", + "fa": "alignment/primary/sharks/GCF_010909765.2.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_010909765.2.repeatModeler.families.fa.gz" + }, + "GCF_017639515.1": { + "2bit": "alignment/primary/sharks/GCF_017639515.1.2bit", + "fa": "alignment/primary/sharks/GCF_017639515.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_017639515.1.repeatModeler.families.fa.gz" + }, + "GCF_020745735.1": { + "2bit": "alignment/primary/sharks/GCF_020745735.1.2bit", + "fa": "alignment/primary/sharks/GCF_020745735.1.fa.gz" + }, + "GCF_030028105.1": { + "2bit": "alignment/primary/sharks/GCF_030028105.1.2bit", + "fa": "alignment/primary/sharks/GCF_030028105.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_030028105.1.repeatModeler.families.fa.gz" + }, + "GCF_030144855.1": { + "2bit": "alignment/primary/sharks/GCF_030144855.1.2bit", + "fa": "alignment/primary/sharks/GCF_030144855.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_030144855.1.repeatModeler.families.fa.gz" + }, + "GCF_030684315.1": { + "2bit": "alignment/primary/sharks/GCF_030684315.1.2bit", + "fa": "alignment/primary/sharks/GCF_030684315.1.fa.gz" + }, + "GCF_035084215.1": { + "2bit": "alignment/primary/sharks/GCF_035084215.1.2bit", + "fa": "alignment/primary/sharks/GCF_035084215.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_035084215.1.repeatModeler.families.fa.gz" + }, + "GCF_036365525.1": { + "2bit": "alignment/primary/sharks/GCF_036365525.1.2bit", + "fa": "alignment/primary/sharks/GCF_036365525.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_036365525.1.repeatModeler.families.fa.gz" + }, + "GCF_036971445.1": { + "2bit": "alignment/primary/sharks/GCF_036971445.1.2bit", + "fa": "alignment/primary/sharks/GCF_036971445.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_036971445.1.repeatModeler.families.fa.gz" + }, + "GCF_044704955.1": { + "2bit": "alignment/primary/sharks/GCF_044704955.1.2bit", + "fa": "alignment/primary/sharks/GCF_044704955.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_044704955.1.repeatModeler.families.fa.gz" + }, + "GCF_902713615.1": { + "2bit": "alignment/primary/sharks/GCF_902713615.1.2bit", + "fa": "alignment/primary/sharks/GCF_902713615.1.fa.gz", + "repeatModeler.families.fa": "alignment/primary/sharks/GCF_902713615.1.repeatModeler.families.fa.gz" + }, + "GCF_008822105.2": { + "2bit": "alignment/secondary/birds/GCF_008822105.2.2bit", + "fa": "alignment/secondary/birds/GCF_008822105.2.fa.gz", + "repeatModeler.families.fa": "alignment/secondary/birds/GCF_008822105.2.repeatModeler.families.fa.gz" + }, + "GCF_015476345.1": { + "2bit": "alignment/secondary/birds/GCF_015476345.1.2bit", + "fa": "alignment/secondary/birds/GCF_015476345.1.fa.gz", + "repeatModeler.families.fa": "alignment/secondary/birds/GCF_015476345.1.repeatModeler.families.fa.gz" + }, + "GCF_016699485.2": { + "2bit": "alignment/secondary/birds/GCF_016699485.2.2bit", + "fa": "alignment/secondary/birds/GCF_016699485.2.fa.gz", + "repeatModeler.families.fa": "alignment/secondary/birds/GCF_016699485.2.repeatModeler.families.fa.gz" + }, + "GCF_010993605.1": { + "2bit": "alignment/secondary/otherChordates/GCF_010993605.1.2bit", + "fa": "alignment/secondary/otherChordates/GCF_010993605.1.fa.gz", + "repeatModeler.families.fa": "alignment/secondary/otherChordates/GCF_010993605.1.repeatModeler.families.fa.gz" + }, + "GCF_040869285.1": { + "2bit": "alignment/secondary/otherChordates/GCF_040869285.1.2bit", + "fa": "alignment/secondary/otherChordates/GCF_040869285.1.fa.gz", + "repeatModeler.families.fa": "alignment/secondary/otherChordates/GCF_040869285.1.repeatModeler.families.fa.gz" + }, + "GCF_000001405.40": { + "2bit": "alignment/secondary/primates/GCF_000001405.40.2bit", + "fa": "alignment/secondary/primates/GCF_000001405.40.fa.gz" + } +} diff --git a/catalog/ga2/source/GenerateExtraFiles.md b/catalog/ga2/source/GenerateExtraFiles.md new file mode 100644 index 00000000..4c951624 --- /dev/null +++ b/catalog/ga2/source/GenerateExtraFiles.md @@ -0,0 +1,14 @@ +# Instruction howto install aws client: +# https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html +# + +aws s3api list-objects-v2 --endpoint-url https://js2.jetstream-cloud.org:8001 --no-sign-request --bucket genomeark --prefix alignment --query "Contents[?contains(Key, '.2bit') || contains(Key, '.fa.gz')].Key" --output json 2>&1 | sed -n '/^\[/{:a;p;n;ba}' | python3 -c "import sys, json, re; +paths=json.load(sys.stdin); +out={}; +for p in paths: + m=re.search(r'(G[CA]F?_\d+\.\d+)', p); + if not m: continue; + key=m.group(1); + ext=p.split(key+'.')[-1].replace('.gz',''); + out.setdefault(key,{})[ext]=p; +json.dump(out, sys.stdout, indent=2)" > AssemblyGenomeArkBucketFile.json