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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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3 2 Sarah Guthrie
{{>toc}}
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5 3 Sarah Guthrie
h3. Creating a Collection
6 1 Sarah Guthrie
7 3 Sarah Guthrie
@arv keep put@
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<pre>
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~$ arv keep put var-GS000016015-ASM.tsv.bz2
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216M / 216M 100.0%
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Collection saved as ...
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qr1hi-4zz18-xxxxxxxxxxxxxxx
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</pre>
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h3. Moving a Collection
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@arv edit@ 
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<pre>
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~$ arv edit qr1hi-4zz18-xxxxxxxxxxxxxxx
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{
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  "uuid": "qr1hi-4zz18-5uhkpoj0zlv3zmu",
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  "owner_uuid": "qr1hi-j7d0g-r0u07fzzlf6dtqq",
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  "created_at": "2016-01-25 19:52:47 UTC",
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  "modified_by_client_uuid": null,
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  "modified_by_user_uuid": "qr1hi-tpzed-tpj2ff66551eyym",
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  "modified_at": "2016-01-25 19:52:47 UTC",
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  "portable_data_hash": "5313e7164bd0ee053b351deefb64408b+32899",
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  "replication_desired": null,
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  "replication_confirmed_at": null,
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  "replication_confirmed": null,
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  "updated_at": null,
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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a6515f3aa8d1379986992e27a90ec7dd+67108864+A7ecf64cdda1c900e9fe29891f5695b541fcef6d7@5734e4ac f64318232d5f1e53e3336b6b5b63441b+67108864+A2c5aaa2703b9b5e6a5b4f10d68ba9f1d5481a04d@5734e4ac 823f3fedc6b457ad61d3376cf4e83d3b+67108864+A6dc156a6dc47ece3aab34249db608eebec788af4@5734e4ac 9bdd43dc3d05cd1e145e69fc9ac08497+67108864+A4beda58b87137685792c6b6529be23a570fbe3e0@5734e4ac 36f57fc22c4e7603534c69c291fa4011+67108864+A67eb3809c0d831721f88b1978e88ad032498eff0@5734e4ac a4a06e51b8979637c2e0e30e49243cc0+67108864+A1e4d093547b117ba43850800fc9badf547cb1d0c@5734e4ac deb7ba919698a8061d7a9da751477193+67108864+A6dcdfafeeb540cfe4fc7ec4077d13d847717a91f@5734e4ac d4e1d08f0698974b78d95e5d5a69b8f7+67108864+A857444e74e7b3659c2a5c1c0638f110fb3d4ccf8@5734e4ac 02afdca63bcaf7355cdc8ff624a3ee6d+67108864+A641eb515129da091088be57c2b4dca1867a934f3@5734e4ac b84cf3a84dfcff696b00fbb4be6a0a18+67108864+Aa994000e6c01d154912e59cd06e5118d060be384@5734e4ac ad57c9e4698e390c50c4f802c5611f3c+67108864+A11f61c465addf3d4859fa86e479773608e7528f5@5734e4ac 11b43cadbdc2c1514f50ae8f327ff795+67108864+A370074eca7872018f7e313cf7499289a82b125f6@5734e4ac f63f3d66029dcaed88601d668a8a50fb+67108864+A4fc78330816b668bc623b7536940b6f31caf0540@5734e4ac 792f6ae043b9614b9a3d5aa4998d6568+67108864+A8822de61c3eee7d51948445b7b795507972a154c@5734e4ac 48a0748f8bbbd585275ff2f1ab1ef9eb+7398552+A5174e6fe9e53c9b85be63c0f04f28160e69a1aa3@5734e4ac 0:6597:GRCh37.fa.amb 6597:6844:GRCh37.fa.ann 13441:3101804844:GRCh37.fa.bwt 3101818285:775451186:GRCh37.fa.pac 3877269471:1550902424:GRCh37.fa.sa\n./genomes/GRCh37/seq 61259557402a36cd1f7ba7d67d9101fb+1200+A7648faf3ac000dc4762dbb0049a2401a462c9ea4@5734e4ac df4c324e0fa6b46bb2dc821a47773693+10257+A574147e1d01215c93d993cc9aa847cd2fcabfc08@5734e4ac 98f626918f20ce4d1eb06f63eb767c6d+67108864+Aca02a73391097dadd6f9ae8ffe6a2d2cea305d6a@5734e4ac 5ed32c6b23ccebcf0f1c5751ba5a7e65+67108864+Ac687abf26508300902df36949c7e4add730e2d15@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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63
  "name": "full genome data",
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  "description": null,
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  "properties": {
66
  },
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  "expires_at": null,
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}
70
</pre>
71
72 1 Sarah Guthrie
73
h3. Other stuff
74
75
other stuff