Only Using the Command Line¶

• Table of contents
• Only Using the Command Line
  • • Creating a Collection
    • Moving a Collection
    • Copying a Collection
    • Other stuff

Creating a Collection¶

arv keep put

~$ arv keep put var-GS000016015-ASM.tsv.bz2
216M / 216M 100.0%
Collection saved as ...
qr1hi-4zz18-xxxxxxxxxxxxxxx

Moving a Collection¶

arv edit

~$ arv edit qr1hi-4zz18-xxxxxxxxxxxxxxx

{
  "uuid": "qr1hi-4zz18-5uhkpoj0zlv3zmu",
  "owner_uuid": "qr1hi-j7d0g-r0u07fzzlf6dtqq",
  "created_at": "2016-01-25 19:52:47 UTC",
  "modified_by_client_uuid": null,
  "modified_by_user_uuid": "qr1hi-tpzed-tpj2ff66551eyym",
  "modified_at": "2016-01-25 19:52:47 UTC",
  "portable_data_hash": "5313e7164bd0ee053b351deefb64408b+32899",
  "replication_desired": null,
  "replication_confirmed_at": null,
  "replication_confirmed": null,
  "updated_at": null,
  "manifest_text": "./genomes/GRCh37/bwa d0279f1ffc0f0b8de3cfc9f5db148897+6597+A1aa59b4a47bae07ecf484bfb5cb4825c75394a5b@5734e4ac c58ec93d555366b1d7e0868c5295c9d3+6844+A214189b570889feb285f8582b15f403fad0e7bb2@5734e4ac d38962ac9cb0dd8bee016d629ddc4b4b+67108864+A65b64017304eff4eff42cbb9791cc0a5c63d0c3a@5734e4ac 42fbe76b0968560b4918e97ad65278d7+67108864+Af4206fc14b985b0a86746612d879f58550898589@5734e4ac 779e0f8f64e2746130af723316b009d9+67108864+Adfa4deb2bfb3c22c05ae61360589cd7e7ce5c6b0@5734e4ac 54e7a46892bc9596c05eacace0373ebe+67108864+Afb1c1332dcfd103e711d487f9653eaf68eec6879@5734e4ac 1f0f6183f55bbf6bac05aca630b684ae+67108864+A8b7b4783d9fcade7fe5ae003afef51ea09a553b4@5734e4ac f87a21f7bdbf77c167570e2caaec5379+67108864+Afefac126063ea3655de91c1e4f10febbad118bd0@5734e4ac 5fe3ee618615435181445ddc5652cdb1+67108864+A17708af7637403d5a8dd4e0715a4968380786a3f@5734e4ac 383135cab8307d6d71951142b95c3762+67108864+A496df5882328695f63b8771b170a419ff1768031@5734e4ac 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22810385:11013364:regulation_GM12878.bin 33823749:8439603:regulation_H1ESC.bin 42263352:5321129:regulation_HMEC.bin 47584481:6148860:regulation_HSMM.bin 53733341:7517190:regulation_HUVEC.bin 61250531:7168143:regulation_HeLa-S3.bin 68418674:10097079:regulation_HepG2.bin 78515753:7641629:regulation_IMR90.bin 86157382:11942848:regulation_K562.bin 98100230:4090811:regulation_NH-A.bin 102191041:7566468:regulation_NHEK.bin 109757509:36288021:sequence.1.bin 146045530:20258734:sequence.10.bin 166304264:21603239:sequence.11.bin 187907503:21941011:sequence.12.bin 209848514:11051564:sequence.13.bin 220900078:14641028:sequence.14.bin 235541106:15743979:sequence.15.bin 251285085:13498628:sequence.16.bin 264783713:14509220:sequence.17.bin 279292933:10948083:sequence.18.bin 290241016:10353400:sequence.19.bin 300594416:37931682:sequence.2.bin 338526098:9101488:sequence.20.bin 347627586:5329491:sequence.21.bin 352957077:6411909:sequence.22.bin 359368986:33244470:sequence.3.bin 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1963696625:1499941:Mills_and_1000G_gold_standard.indels.vcf.gz.tbi 1965196566:20428786:cosmic-v68-GRCh37.vcf.gz 1985625352:910614:cosmic-v68-GRCh37.vcf.gz.tbi 1986535966:1553160134:dbsnp_138.vcf.gz 3539696100:2289759:dbsnp_138.vcf.gz.tbi 3541985859:61264826:hapmap_3.3.vcf.gz 3603250685:1556535:hapmap_3.3.vcf.gz.tbi 3604807220:874804773:human_ancestor.fa.gz 4479611993:736:human_ancestor.fa.gz.fai 4479612729:766344:human_ancestor.fa.gz.gzi 4480379073:66792457:qsignature.vcf\n",
  "name": "full genome data",
  "description": null,
  "properties": {
  },
  "expires_at": null,
  "file_names": null
}

Copying a Collection¶

arv create collection

{
  "uuid": "qr1hi-4zz18-5uhkpoj0zlv3zmu",
  "owner_uuid": "qr1hi-j7d0g-r0u07fzzlf6dtqq",
  "created_at": "2016-01-25 19:52:47 UTC",
  "modified_by_client_uuid": null,
  "modified_by_user_uuid": "qr1hi-tpzed-tpj2ff66551eyym",
  "modified_at": "2016-01-25 19:52:47 UTC",
  "portable_data_hash": "5313e7164bd0ee053b351deefb64408b+32899",
  "replication_desired": null,
  "replication_confirmed_at": null,
  "replication_confirmed": null,
  "updated_at": null,
  "manifest_text": "./genomes/GRCh37/bwa d0279f1ffc0f0b8de3cfc9f5db148897+6597+A1aa59b4a47bae07ecf484bfb5cb4825c75394a5b@5734e4ac c58ec93d555366b1d7e0868c5295c9d3+6844+A214189b570889feb285f8582b15f403fad0e7bb2@5734e4ac d38962ac9cb0dd8bee016d629ddc4b4b+67108864+A65b64017304eff4eff42cbb9791cc0a5c63d0c3a@5734e4ac 42fbe76b0968560b4918e97ad65278d7+67108864+Af4206fc14b985b0a86746612d879f58550898589@5734e4ac 779e0f8f64e2746130af723316b009d9+67108864+Adfa4deb2bfb3c22c05ae61360589cd7e7ce5c6b0@5734e4ac 54e7a46892bc9596c05eacace0373ebe+67108864+Afb1c1332dcfd103e711d487f9653eaf68eec6879@5734e4ac 1f0f6183f55bbf6bac05aca630b684ae+67108864+A8b7b4783d9fcade7fe5ae003afef51ea09a553b4@5734e4ac f87a21f7bdbf77c167570e2caaec5379+67108864+Afefac126063ea3655de91c1e4f10febbad118bd0@5734e4ac 5fe3ee618615435181445ddc5652cdb1+67108864+A17708af7637403d5a8dd4e0715a4968380786a3f@5734e4ac 383135cab8307d6d71951142b95c3762+67108864+A496df5882328695f63b8771b170a419ff1768031@5734e4ac 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22810385:11013364:regulation_GM12878.bin 33823749:8439603:regulation_H1ESC.bin 42263352:5321129:regulation_HMEC.bin 47584481:6148860:regulation_HSMM.bin 53733341:7517190:regulation_HUVEC.bin 61250531:7168143:regulation_HeLa-S3.bin 68418674:10097079:regulation_HepG2.bin 78515753:7641629:regulation_IMR90.bin 86157382:11942848:regulation_K562.bin 98100230:4090811:regulation_NH-A.bin 102191041:7566468:regulation_NHEK.bin 109757509:36288021:sequence.1.bin 146045530:20258734:sequence.10.bin 166304264:21603239:sequence.11.bin 187907503:21941011:sequence.12.bin 209848514:11051564:sequence.13.bin 220900078:14641028:sequence.14.bin 235541106:15743979:sequence.15.bin 251285085:13498628:sequence.16.bin 264783713:14509220:sequence.17.bin 279292933:10948083:sequence.18.bin 290241016:10353400:sequence.19.bin 300594416:37931682:sequence.2.bin 338526098:9101488:sequence.20.bin 347627586:5329491:sequence.21.bin 352957077:6411909:sequence.22.bin 359368986:33244470:sequence.3.bin 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  "name": "full genome data",
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  "properties": {
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}

Other stuff¶

other stuff