Only Using the Command Line » History » Version 3
Sarah Guthrie, 04/28/2016 08:53 PM
| 1 | 1 | Sarah Guthrie | h1. Only Using the Command Line |
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| 2 | |||
| 3 | 2 | Sarah Guthrie | {{>toc}} |
| 4 | |||
| 5 | 3 | Sarah Guthrie | h3. Creating a Collection |
| 6 | 1 | Sarah Guthrie | |
| 7 | 3 | Sarah Guthrie | @arv keep put@ |
| 8 | |||
| 9 | <pre> |
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| 10 | ~$ arv keep put var-GS000016015-ASM.tsv.bz2 |
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| 11 | 216M / 216M 100.0% |
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| 12 | Collection saved as ... |
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| 13 | qr1hi-4zz18-xxxxxxxxxxxxxxx |
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| 14 | </pre> |
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| 15 | |||
| 16 | h3. Moving a Collection |
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| 17 | |||
| 18 | @arv edit@ |
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| 19 | |||
| 20 | <pre> |
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| 21 | ~$ arv edit qr1hi-4zz18-xxxxxxxxxxxxxxx |
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| 22 | |||
| 23 | { |
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| 24 | "uuid": "qr1hi-4zz18-5uhkpoj0zlv3zmu", |
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| 25 | "owner_uuid": "qr1hi-j7d0g-r0u07fzzlf6dtqq", |
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| 26 | "created_at": "2016-01-25 19:52:47 UTC", |
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| 27 | "modified_by_client_uuid": null, |
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| 28 | "modified_by_user_uuid": "qr1hi-tpzed-tpj2ff66551eyym", |
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| 29 | "modified_at": "2016-01-25 19:52:47 UTC", |
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| 30 | "portable_data_hash": "5313e7164bd0ee053b351deefb64408b+32899", |
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| 31 | "replication_desired": null, |
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| 32 | "replication_confirmed_at": null, |
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| 33 | "replication_confirmed": null, |
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| 34 | "updated_at": null, |
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| 35 | "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", |
||
| 36 | "name": "full genome data", |
||
| 37 | "description": null, |
||
| 38 | "properties": { |
||
| 39 | }, |
||
| 40 | "expires_at": null, |
||
| 41 | "file_names": null |
||
| 42 | } |
||
| 43 | </pre> |
||
| 44 | |||
| 45 | h3. Copying a Collection |
||
| 46 | |||
| 47 | @arv create collection@ |
||
| 48 | |||
| 49 | <pre> |
||
| 50 | { |
||
| 51 | "uuid": "qr1hi-4zz18-5uhkpoj0zlv3zmu", |
||
| 52 | "owner_uuid": "qr1hi-j7d0g-r0u07fzzlf6dtqq", |
||
| 53 | "created_at": "2016-01-25 19:52:47 UTC", |
||
| 54 | "modified_by_client_uuid": null, |
||
| 55 | "modified_by_user_uuid": "qr1hi-tpzed-tpj2ff66551eyym", |
||
| 56 | "modified_at": "2016-01-25 19:52:47 UTC", |
||
| 57 | "portable_data_hash": "5313e7164bd0ee053b351deefb64408b+32899", |
||
| 58 | "replication_desired": null, |
||
| 59 | "replication_confirmed_at": null, |
||
| 60 | "replication_confirmed": null, |
||
| 61 | "updated_at": null, |
||
| 62 | "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", |
||
| 63 | "name": "full genome data", |
||
| 64 | "description": null, |
||
| 65 | "properties": { |
||
| 66 | }, |
||
| 67 | "expires_at": null, |
||
| 68 | "file_names": null |
||
| 69 | } |
||
| 70 | </pre> |
||
| 71 | |||
| 72 | 1 | Sarah Guthrie | |
| 73 | h3. Other stuff |
||
| 74 | |||
| 75 | other stuff |