The following examples demonstrate the commands in the BaseSpace CLI tool. For more information about the CLI and a list of commands, see CLI Overview.

Authentication, listing projects and appresults

Install:

See main instructions.

Authenticate using default settings:

$ bs auth                                                           
Please go to this URL to authenticate:                                
https://basespace.illumina.com/oauth/device?code=jfHSG                
Created config file /home/psaffrey/.basespace/default.cfg             
Welcome, BSSH.V2 TestUser                                             

Inspect the token to see what it does:

Example:

$bs whoami
+----------------+-------------------------------------------------+
| Name           | BaseSpace User                                  |
| Id             | 1234567                                         |
| Email          | basespaceuser@illumina.com                      |
| DateCreated    | 2015-01-16 15:31:22 +0000 UTC                   |
| DateLastActive | 2017-06-01 12:59:24 +0000 UTC                   |
| Host           | https://api.basespace.illumina.com              |
| Scopes         | ["READ GLOBAL" "CREATE GLOBAL" "BROWSE GLOBAL"] |
+----------------+-------------------------------------------------+

List projects:

$ bs list projects   
+--------------------------------------------------+----------+---------------+
|                       Name                       |    Id    |   TotalSize   |
+--------------------------------------------------+----------+---------------+
| NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | 36080093 | 2233311909088 |
+--------------------------------------------------+----------+---------------+

List datasets:

$ bs list datasets
+--------------------------+-------------------------------------+--------------------------------------------------+---------------------+
|           Name           |                 Id                  |                   Project.Name                   |   DataSetType.Id    |
+--------------------------+-------------------------------------+--------------------------------------------------+---------------------+
| NA12878-I13_L002         | ds.184ba3d796f343f4886b4aa7fb43c496 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I13_L001         | ds.c805113ed9884caa8912dafdf8edd63d | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I54_L001         | ds.dc5657d91983479eb0dd6abb53b9d60f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I85_L001         | ds.0a7781b4d7684113a4c64c1f2ca3c175 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I87_L001         | ds.17350079cfb7445fbb29848443f7a975 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I5_L002          | ds.27592c7405e44e87ba67a829b0f05ed6 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I92_L002         | ds.6bb3c9761f7c4c7fb034e2b50231a029 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I41_L002         | ds.9c9560c5e91047808511f245c2c4e5c5 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I56_L001         | ds.46785e11c6ad4a2cba55bbd1935635c0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I34_L001         | ds.355febad8f7a4f5584ab4a1864eb434c | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I41_L001         | ds.ef9fb11028174530a4a2eb27efae2c29 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I25_L001         | ds.f0b5644ab5784329aa5490688d9a80b9 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I51_L001         | ds.ca44ebdff3384b5bb21b585a59fd109c | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I67_L001         | ds.94b469660ef94c14ae2c53be2fab1bda | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I85_L002         | ds.8b4cc1498a4749ada8e0a71c90d19e00 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I87_L002         | ds.579986a9924d420ab88309c2fc44632a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I54_L002         | ds.1e878a2fa9d54dd2b2bfbe153f942776 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I30_L001         | ds.4d8d0244605f469f90281b03f2312f6f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I18_L002         | ds.cfd63d4272164b3cab5f3608c1442162 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I18_L001         | ds.ef78dcde564c421184f82bf2de738b5d | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I25_L002         | ds.73c4978e6b8f49c8a73ee53e258b215a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I21_L002         | ds.01b4bbbe2f044f62a10410ea3c022c00 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I31_L002         | ds.4237d0fdd25e400c8bdd317a0aa2c7ea | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I12_L002         | ds.616586c597f3474d9adeaa16216c3ff9 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I31_L001         | ds.5dd764b70a8a4bd19fc51d23a221224d | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I12_L001         | ds.a632faf8590141c6b660b289dbae9ff9 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I2_L002          | ds.239f741d085c4ea8943289005b4a60e1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I51_L002         | ds.9ed5549041e047a7865143402c148690 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I67_L002         | ds.ebb75108df5c40ad9288c9b570f81f41 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I56_L002         | ds.ce63f3b9ed8b49daa6fbe3fdc00a6db4 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I30_L002         | ds.9a76e80d44e0495599d0234084e3cf89 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I34_L002         | ds.437655a23add43e8bbf892b0ded4ed91 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I86_L001         | ds.f5a0e27630914f2091d298e3c24c968c | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I47_L001         | ds.7e872704e95f43d9989f3f96dc705db4 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I76_L002         | ds.05a7a58a21a045e8a13329cedb7d321f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I48_L002         | ds.479660a878ff4b898bb73648825a92c2 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I76_L001         | ds.06f09a3d9d4e4fd6bc951d8179ac370f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I48_L001         | ds.c94916c31de34e59ab8ebaaeccae3c02 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I86_L002         | ds.93f3f9a3062442bab199140d1689e6b7 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I47_L002         | ds.e06da408442d416b8a41d362e7365f52 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I80_L001         | ds.177ae7be15a6416e88018f6d3ae758e4 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I78_L001         | ds.2a29c6c68bcf471f915d51102f276ad1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I32_L002         | ds.707e69bf6ef14c6e9b2f4421458d77b1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I32_L001         | ds.5b29cb054d7c4e4c9ba04629f5b1ceb9 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I91_L001         | ds.026eb1b58eac4530a5078eb0d19c2ade | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I93_L001         | ds.08b8d1425e0b48f6a8f0d7338a46e076 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I78_L002         | ds.83535361f01c410abbbc9d4fe83b7448 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I80_L002         | ds.f0c26644bf554490b7362880f5242f0b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I24_L001         | ds.e3caa736c6c74dc49d04e84bd7023f95 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I8_L001          | ds.f3d83a3e464d4b11bd924feeaaf02417 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I93_L002         | ds.4608dca6ea4e4a44b6f0309960994d9f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I29_L002         | ds.df4c55504e9848039a7c1ed2ac9648ee | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I91_L002         | ds.11fc63df3d364086bb94e228630f787e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I29_L001         | ds.2fba3884629a4be5b3bd50bf76f4f4f4 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I24_L002         | ds.ab4b5e74bd054c86b6071e4b5348e51e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I8_L002          | ds.d1fd0c6ae47f4c1ea2dc5ea4267a1bc2 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I72_L001         | ds.84a7894efdd64d5490f28e06657c47d6 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I72_L002         | ds.51ec8ce8e8dd4a2385cd33ac06f3203f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I96_L001         | ds.46c5b7f9e52f433887ad2342278d7354 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I82_L001         | ds.d231f6aeb233490cabeb5a3316fab3fd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I96_L002         | ds.a495ff254920449b8958a1cc1bb01d5a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I82_L002         | ds.f4970b7daf4c453882605a393f700cbd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I42_L001         | ds.02e52614edeb4c09861a37c30ce0d8be | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I40_L001         | ds.16d7fb364c544696886acf593b719667 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I37_L001         | ds.4244c6a1baef4a9a88021ce4460baf3e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I42_L002         | ds.1936704ba9c140e4b13114c6ebda1555 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I40_L002         | ds.33a48fdf8e034b9a8d28197829b6a1c3 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I90_L001         | ds.1560e453d9cf4c65947ffcfa90ab57ca | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I7_L002          | ds.14d5d9fa4f7d406493a28aa93b7e3f9e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I17_L001         | ds.bb22161d44154f1dbb00f77ee232975f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I71_L002         | ds.345db76f12334b969683ba605e9a0a87 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I7_L001          | ds.d69d360328f6438ea590fefe26718b7a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I71_L001         | ds.d0efa5a6560248728a32664bbb8ceca8 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I64_L002         | ds.8f4cb219ac1243a29419a1fdbdc4673a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I64_L001         | ds.eca4280bfba24b37ab89f4b9a525259b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I20_L002         | ds.4cfc5e55478c4d2cbdf8e93f3d7e45df | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I20_L001         | ds.79ffb387199e47629cd84d2101defacc | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I37_L002         | ds.835641fe405d4093986ad256f27bd2c0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I90_L002         | ds.1096d83cac9140598de8cffffdd9092b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I61_L001         | ds.46a9d2b5a371468093284296bd1756f1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I73_L001         | ds.536eabf911ae4b679fc7b51c22742100 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I38_L001         | ds.aa934975957642138c3858a840faca41 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I69_L001         | ds.7929dfce40c64ce9b043834244d5049d | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I68_L001         | ds.b980a0d0c66d4dbb9aa7188e1ab2f7cc | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I33_L001         | ds.f778f3a77b494f06a6baba136a6de8bd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I44_L002         | ds.a98be176c4ac4c0693c432d77060a259 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I44_L001         | ds.562283b784f54f83b1bb5c918f2cc690 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I61_L002         | ds.0b0ec3b54c554872baf8e623f8c00336 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I17_L002         | ds.ab3e1fef2ecc4ac68a88e557942e4d90 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I73_L002         | ds.9617eaec7de4456b9b079aa4bd7b14f2 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I38_L002         | ds.b1c3d9af049441f2aea8bc428132b334 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I69_L002         | ds.32c4b171c3af4a43948bb34f3cb3fcb2 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I68_L002         | ds.b5878be0ea704e8182d7fe56a04d8981 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I52_L001         | ds.0ed18990c01249bc9af3603098787d5e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I53_L001         | ds.8dc523d654154601a9a82d53a429e2d9 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I1_L001          | ds.1ae2d4d97c4d4db682cae3e9a178a15a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I33_L002         | ds.38969167545a41508c4f6abe5bc8824c | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I39_L001         | ds.c1c41fd2a8e14e319eb136b931c65452 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I3_L002          | ds.91d6c5c60e184dadaeaedfcf0e3bbb31 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I3_L001          | ds.ed0b35ca14b3425d8ebd6921bdc283bf | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I63_L002         | ds.45af7844d36342478f7d5ba8a58bfe4b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I58_L002         | ds.b5a70d8bfa6a4152b918314692586fe1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I63_L001         | ds.2ea1384e7a184b8fb9e1df7c4693242e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I58_L001         | ds.c5a13fe1640744ab9c36fddc35df4c54 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I52_L002         | ds.5e9685172e784daabecfcb222cccc88e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I1_L002          | ds.2bc41b20deab4e01842cc4a957f090f0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I53_L002         | ds.45d151abd8f74083926dcfbb59534ecc | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I19_L001         | ds.a68838a426ac4bbfbf3ec6b76c65e1c5 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I6_L001          | ds.125e2d2b0f334257ae7ae5fa05e4b1fb | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I6_L002          | ds.061cfcca0c524ba59a172d51ed758820 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I19_L002         | ds.bb04f02618bf4146a3192c7727874e62 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I39_L002         | ds.2cf74999dfe9477bb0a4098680803551 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I22_L001         | ds.65e29343ec2741148ce66bf457b8c6c7 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I94_L001         | ds.f8a45574647d450a8f8b811c3ddbb1b7 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I62_L002         | ds.dfb1636e81474dd1b3b49cc8990237dd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I57_L002         | ds.0db7a2e19b98441ebe72b82aacc784df | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I57_L001         | ds.b7aed51f6285477db28ea8e98e2abe1d | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I62_L001         | ds.d1e92c2b494d4e17b1be229055faddb9 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I59_L001         | ds.ffe619cee21a4012bd0f7ce04f97f386 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I79_L002         | ds.d1f05f563fc74ada974ad2f590c99a5f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I22_L002         | ds.73fa6dc628d640a893327df6a4b169d0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I79_L001         | ds.33c002b03bab4f998e166290217bdffc | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I95_L001         | ds.a5dcff66919e47d59120f11e98479f7b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I28_L001         | ds.a399fe4ffae44ae5923cd6d293e8b217 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I16_L002         | ds.5c538ce9f59b422a830e5824763e1c6a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I89_L002         | ds.67aa5a0bbaca414bb97f5c0ed2c6c34a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I43_L002         | ds.9c00ad1a6d5a49fea41dab2534153893 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I16_L001         | ds.8ea461235a294d769469b17e1b227616 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I43_L001         | ds.d0cf22791742445a82beae4744c8e1b0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I89_L001         | ds.f0d2153c42da4aa0bc3a9e14077a3f43 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I9_L001          | ds.e38993ed64ea432a8244a1ed34dedc36 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I84_L001         | ds.90d1fa5028654066b1f8f94f6e588922 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I94_L002         | ds.62197f6fdf3841a5968afe935f5439e0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I95_L002         | ds.d161ea7a25e145df992326c48c997771 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I28_L002         | ds.2b0701db93ae4dc6b3fbbf9f4c0cf63e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I27_L001         | ds.70a3612de35c4dc3a91ebb62a4c68721 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I65_L001         | ds.f2237aa1fea74203b04d22af67373648 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I9_L002          | ds.207f097542444390990d7be6e4012ef2 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I59_L002         | ds.8b3d3f5dfea749129066e3c5e9de16fd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I84_L002         | ds.dcfa719695da4e058d898ddd24db9606 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I27_L002         | ds.89c91ee4dbab41ed8db82c727dabc971 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I65_L002         | ds.d1d8e363971946b2b56471416d16b5d4 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I66_L002         | ds.790ed00d2dbc448f870133bbc1f10cab | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I55_L002         | ds.3f522d2d4f6b44c2990b08b0e7266d4a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I36_L002         | ds.ff4212332da544bbbedd9cee7b8f2a94 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I66_L001         | ds.943a22628e6445beb9b435e5e5b9b145 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I55_L001         | ds.e28bb97ce19c4a6c85d57e952bfff542 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I36_L001         | ds.d3005639840244c889f57af09d70c384 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I81_L001         | ds.f98c4856bca144babd9f25db2010f717 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I46_L001         | ds.112d777c43d84139b03296302415f1df | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I83_L001         | ds.c42f30c0557742d09baf5038aec407b0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I81_L002         | ds.f42f222baaac476b8c3668aeedd569da | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I83_L002         | ds.9e5c9a8089ae43f7a8a07d61f6cdcafe | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I46_L002         | ds.11fdf04d6ef84580939442015168f152 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I4_L002          | ds.1b7727b649ce4c43ab6352fc8d91974b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I10_L002         | ds.af4c5466c16a48d0b37bdb6aa49509b5 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I50_L001         | ds.9de23a07337a4798bc0a1daceeb92bb3 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I10_L001         | ds.233489d6e9ef48cca09c1de9c8c7d1ae | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I4_L001          | ds.11c2092c1d3f4f7c89abf564311ef16b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I50_L002         | ds.2f5b56dddc0440858943246ba4ac9d11 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I23_L002         | ds.5afb36c9a59a40e9b5184519984ec0a2 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I23_L001         | ds.c72648b99d56462eb6cfb337e78344af | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I45_L002         | ds.8334055c689a4e798fb66f672b9dbdee | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I45_L001         | ds.fac241934ea0495f850df89b552550fd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I75_L001         | ds.bf7ded32eff64d549c7a94e1bb9d2940 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I75_L002         | ds.60c487c2f71c4b2f83b0651b3b1cb8de | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I14_L001         | ds.d8618ca59d0b43ed89fa2e2c8e5c63fb | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I88_L001         | ds.d9184799d60a43749b2b48d28a0a0fe6 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I49_L001         | ds.762e442c9b5942688829e0fd041d0134 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I70_L002         | ds.c170ce38cab747abadd921bf7d116ebd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I70_L001         | ds.499020097f5b424e8fb586cac368f7af | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I14_L002         | ds.4af1d2e33bc0473eaa33b2430824ff06 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I60_L001         | ds.438172565c0945f2b87798192d4d00ee | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I49_L002         | ds.8a020bbcb4ee4f908f9d7497102a5964 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I88_L002         | ds.ba8a247aaf8946028e13de9e0399bbca | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I60_L002         | ds.694194f9c8604a9fb3bc6931b304421f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-R8               | ds.1e4edcca5ee6492e97c9b11cfca16a19 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R6               | ds.79ecd6fa647b456484668edcbc455008 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R7               | ds.0aa58bc16b2549a4b9e5682d00c6c6d0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R3               | ds.2f0c171083e44fc99fd8f9c1994b7ac3 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R5               | ds.e29fae0f705348b78b31f35004bb97ab | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R4               | ds.f7360ed9ed984bfcbf4da39bcd580581 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R1               | ds.61e5fceeeb0b48ce9967a0effe09ace3 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R2               | ds.3be316eb0c3d44a8a76b3e1fca8ac2ee | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R1S1vcf-38337470 | ds.f45e4fcccbce4fb18dd91bdad7dcb272 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R2S1vcf-38347407 | ds.ad8cdba7884e4665af6ce6e4b9eda394 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R7S1vcf-38332429 | ds.521b04555c2244aa8d2bb8eb821a5ed7 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R3S1vcf-38334439 | ds.fa5fb81a631940caace69197a3fa37f7 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R5S1vcf-38332433 | ds.05fefa9dae274e459281b2e2ec3bdba1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R4S1vcf-38337469 | ds.84dfccff8bc046c8b1bc44900891a69a | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R6S1vcf-38345414 | ds.e8297c4026194759a24c61960137b1c0 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R8S1vcf-38345413 | ds.71b8d3f02edf43858bbc35f55989a422 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R8               | ds.bad9b1fc7ac246cdbf73ee7c924e36bf | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R7               | ds.5a6db37aa1474a6e9e8438ba33feb47c | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R6               | ds.7286aa0681ee4d269483c99cd976afcc | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R4               | ds.64a06c23936642d2aac2431640abe21e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R5               | ds.ad3647050baa47dab52ee0553b5c708e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R2               | ds.3732c67232cd431083fa13e6ad32f721 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R1               | ds.87707baabfc048669d8b56d8560a7e7b | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-R3               | ds.db09fe6c93a74935808666f60b1bc96f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | common.files        |
| NA12878-I77_L001         | ds.169df23440984f5081bc38d6ca630df7 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I11_L001         | ds.d629085ed4af4fb991059fbfb4169588 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I15_L002         | ds.e551217ad57145c7b93206eb9a37df1f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I5_L001          | ds.047d006525df4908b1d86f92eca0aba1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I92_L001         | ds.b1e6a4aa70a747e88ffade8c04102aa1 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I15_L001         | ds.b0533b4e96f9420380bcbe595ce7cadd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I21_L001         | ds.98d2ed48ad204f619c79b88bdfb9b93f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I26_L002         | ds.32c15ce8a38c4121a935c883e903f9eb | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I77_L002         | ds.5d67169a8a3c4c13b9eab46b7f244a7f | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I11_L002         | ds.982c0ce5ce334a06931057b41b9b48e6 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I26_L001         | ds.5e9a458f9c7a4f42b5410917f9b531bd | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I2_L001          | ds.5c70c5f1a6f0452f9d7cbfc74b484055 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I74_L002         | ds.6c72500ddec6472dad547d2f412942e4 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I74_L001         | ds.bb81e6ad578040ed9ed0d8650589585c | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I35_L002         | ds.1b2d8472829348f5a2988d9f1ccd5465 | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
| NA12878-I35_L001         | ds.6c10e969aa294120a30a755624795a6e | NovaSeq: TruSeq Nano 550 (Replicates of NA12878) | illumina.fastq.v1.8 |
+--------------------------+-------------------------------------+--------------------------------------------------+---------------------+

List all the available headers for datasets:

$ bs dataset headers                                                 
[                                                                    
    "Id",                                                                 
    "Name",                                                               
    "AppSession.Id",                                                      
    "AppSession.Name",                                                    
    "AppSession.Application.AppFamilySlug",                               
    "AppSession.Application.AppVersionSlug",                              
    "AppSession.Application.Id",                                          
    "AppSession.Application.VersionNumber",                               
    "AppSession.Application.HomepageUri",                                 
    "AppSession.Application.ShortDescription",                            
    "AppSession.Application.LongDescription",                             
    "AppSession.Application.Category",                                    
    "AppSession.Application.UserOwnedBy.Id",                              
    "AppSession.Application.UserOwnedBy.Name",                            
    "AppSession.Application.UserOwnedBy.GravatarURL",                     
    "AppSession.Application.UserOwnedBy.DateLastActive",                  
    "AppSession.Application.UserOwnedBy.DateCreated",                     
    "AppSession.Application.Name",                                        
    "AppSession.Application.CompanyName",                                 
    "AppSession.ExecutionStatus",                                         
    "AppSession.QcStatus",                                                
    "AppSession.DeliveryStatus",                                          
    "AppSession.UserCreatedBy.Id",                                        
    "AppSession.UserCreatedBy.Name",                                      
    "AppSession.UserCreatedBy.GravatarURL",                               
    "AppSession.UserCreatedBy.DateLastActive",                            
    "AppSession.UserCreatedBy.DateCreated",                               
    "AppSession.StatusSummary",                                           
    "AppSession.TotalSize",                                               
    "Project.Name",                                                       
    "Project.Id",                                                         
    "Project.Description",                                                
    "Project.TotalSize",                                                  
    "UserOwnedBy.Id",                                                     
    "UserOwnedBy.Name",                                                   
    "UserOwnedBy.GravatarURL",                                            
    "UserOwnedBy.DateLastActive",                                         
    "UserOwnedBy.DateCreated",                                            
    "DataSetType.Id",                                                     
    "DataSetType.Name",                                                   
    "QcStatus",                                                           
    "QcStatusSummary",                                                    
    "UploadStatus",                                                       
    "UploadStatusSummary",                                                
    "ValidationStatus",                                                   
    "TotalSize"                                                           
 ] 
 

Relist all datasets

Using custom columns selected from the headers list:

$ bs list datasets -F Name -F QcStatus -F TotalSize -F AppSession.Application.Name                                           
+--------------------------+-----------+-------------+---------------------------------+
|           Name           | QcStatus  |  TotalSize  |   AppSession.Application.Name   |
+--------------------------+-----------+-------------+---------------------------------+
| NA12878-I13_L002         | Undefined | 4047606231  | FASTQ Generation                |
| NA12878-I13_L001         | Undefined | 4118853581  | FASTQ Generation                |
| NA12878-I54_L001         | Undefined | 3496655065  | FASTQ Generation                |
| NA12878-I85_L001         | Undefined | 2462111619  | FASTQ Generation                |
| NA12878-I87_L001         | Undefined | 2271497152  | FASTQ Generation                |
| NA12878-I5_L002          | Undefined | 3577507440  | FASTQ Generation                |
| NA12878-I92_L002         | Undefined | 2112928928  | FASTQ Generation                |
| NA12878-I41_L002         | Undefined | 3632881869  | FASTQ Generation                |
| NA12878-I56_L001         | Undefined | 3224094016  | FASTQ Generation                |
| NA12878-I34_L001         | Undefined | 4116459968  | FASTQ Generation                |
| NA12878-I41_L001         | Undefined | 3694152200  | FASTQ Generation                |
| NA12878-I25_L001         | Undefined | 3747091707  | FASTQ Generation                |
| NA12878-I51_L001         | Undefined | 3958306719  | FASTQ Generation                |
| NA12878-I67_L001         | Undefined | 2370964606  | FASTQ Generation                |
| NA12878-I85_L002         | Undefined | 2419462073  | FASTQ Generation                |
| NA12878-I87_L002         | Undefined | 2232973035  | FASTQ Generation                |
| NA12878-I54_L002         | Undefined | 3434285896  | FASTQ Generation                |
| NA12878-I30_L001         | Undefined | 2880374312  | FASTQ Generation                |
| NA12878-I18_L002         | Undefined | 3590806026  | FASTQ Generation                |
| NA12878-I18_L001         | Undefined | 3650324167  | FASTQ Generation                |
| NA12878-I25_L002         | Undefined | 3690483226  | FASTQ Generation                |
| NA12878-I21_L002         | Undefined | 4157489454  | FASTQ Generation                |
| NA12878-I31_L002         | Undefined | 2876180903  | FASTQ Generation                |
| NA12878-I12_L002         | Undefined | 4680359907  | FASTQ Generation                |
| NA12878-I31_L001         | Undefined | 2926568314  | FASTQ Generation                |
| NA12878-I12_L001         | Undefined | 4755454462  | FASTQ Generation                |
| NA12878-I2_L002          | Undefined | 3173203626  | FASTQ Generation                |
| NA12878-I51_L002         | Undefined | 3888565944  | FASTQ Generation                |
| NA12878-I67_L002         | Undefined | 2328286368  | FASTQ Generation                |
| NA12878-I56_L002         | Undefined | 3161928470  | FASTQ Generation                |
| NA12878-I30_L002         | Undefined | 2834719725  | FASTQ Generation                |
| NA12878-I34_L002         | Undefined | 4053830415  | FASTQ Generation                |
| NA12878-I86_L001         | Undefined | 2713269607  | FASTQ Generation                |
| NA12878-I47_L001         | Undefined | 3648813128  | FASTQ Generation                |
| NA12878-I76_L002         | Undefined | 2627774092  | FASTQ Generation                |
| NA12878-I48_L002         | Undefined | 4250662193  | FASTQ Generation                |
| NA12878-I76_L001         | Undefined | 2664031207  | FASTQ Generation                |
| NA12878-I48_L001         | Undefined | 4318152210  | FASTQ Generation                |
| NA12878-I86_L002         | Undefined | 2665118606  | FASTQ Generation                |
| NA12878-I47_L002         | Undefined | 3583487479  | FASTQ Generation                |
| NA12878-I80_L001         | Undefined | 3068676911  | FASTQ Generation                |
| NA12878-I78_L001         | Undefined | 2408609667  | FASTQ Generation                |
| NA12878-I32_L002         | Undefined | 2844155023  | FASTQ Generation                |
| NA12878-I32_L001         | Undefined | 2892232520  | FASTQ Generation                |
| NA12878-I91_L001         | Undefined | 2153610715  | FASTQ Generation                |
| NA12878-I93_L001         | Undefined | 3159586478  | FASTQ Generation                |
| NA12878-I78_L002         | Undefined | 2366550832  | FASTQ Generation                |
| NA12878-I80_L002         | Undefined | 3013366427  | FASTQ Generation                |
| NA12878-I24_L001         | Undefined | 5004245648  | FASTQ Generation                |
| NA12878-I8_L001          | Undefined | 3549320884  | FASTQ Generation                |
| NA12878-I93_L002         | Undefined | 3107719561  | FASTQ Generation                |
| NA12878-I29_L002         | Undefined | 2751330335  | FASTQ Generation                |
| NA12878-I91_L002         | Undefined | 2113394087  | FASTQ Generation                |
| NA12878-I29_L001         | Undefined | 2793021729  | FASTQ Generation                |
| NA12878-I24_L002         | Undefined | 4924536845  | FASTQ Generation                |
| NA12878-I8_L002          | Undefined | 3485601302  | FASTQ Generation                |
| NA12878-I72_L001         | Undefined | 3665430083  | FASTQ Generation                |
| NA12878-I72_L002         | Undefined | 3611648928  | FASTQ Generation                |
| NA12878-I96_L001         | Undefined | 3153973722  | FASTQ Generation                |
| NA12878-I82_L001         | Undefined | 3695194463  | FASTQ Generation                |
| NA12878-I96_L002         | Undefined | 3103080061  | FASTQ Generation                |
| NA12878-I82_L002         | Undefined | 3635097354  | FASTQ Generation                |
| NA12878-I42_L001         | Undefined | 3595976168  | FASTQ Generation                |
| NA12878-I40_L001         | Undefined | 3463789417  | FASTQ Generation                |
| NA12878-I37_L001         | Undefined | 3699651215  | FASTQ Generation                |
| NA12878-I42_L002         | Undefined | 3536199374  | FASTQ Generation                |
| NA12878-I40_L002         | Undefined | 3418677260  | FASTQ Generation                |
| NA12878-I90_L001         | Undefined | 2454010601  | FASTQ Generation                |
| NA12878-I7_L002          | Undefined | 4063229732  | FASTQ Generation                |
| NA12878-I17_L001         | Undefined | 3994779028  | FASTQ Generation                |
| NA12878-I71_L002         | Undefined | 2743543818  | FASTQ Generation                |
| NA12878-I7_L001          | Undefined | 4135943497  | FASTQ Generation                |
| NA12878-I71_L001         | Undefined | 2790728928  | FASTQ Generation                |
| NA12878-I64_L002         | Undefined | 2646657634  | FASTQ Generation                |
| NA12878-I64_L001         | Undefined | 2679491538  | FASTQ Generation                |
| NA12878-I20_L002         | Undefined | 3655996458  | FASTQ Generation                |
| NA12878-I20_L001         | Undefined | 3722332850  | FASTQ Generation                |
| NA12878-I37_L002         | Undefined | 3637273258  | FASTQ Generation                |
| NA12878-I90_L002         | Undefined | 2410146097  | FASTQ Generation                |
| NA12878-I61_L001         | Undefined | 2795508796  | FASTQ Generation                |
| NA12878-I73_L001         | Undefined | 3003902756  | FASTQ Generation                |
| NA12878-I38_L001         | Undefined | 4087228709  | FASTQ Generation                |
| NA12878-I69_L001         | Undefined | 3132872515  | FASTQ Generation                |
| NA12878-I68_L001         | Undefined | 2445090043  | FASTQ Generation                |
| NA12878-I33_L001         | Undefined | 3526971619  | FASTQ Generation                |
| NA12878-I44_L002         | Undefined | 3029071991  | FASTQ Generation                |
| NA12878-I44_L001         | Undefined | 3084644043  | FASTQ Generation                |
| NA12878-I61_L002         | Undefined | 2751023964  | FASTQ Generation                |
| NA12878-I17_L002         | Undefined | 3929520398  | FASTQ Generation                |
| NA12878-I73_L002         | Undefined | 2950263595  | FASTQ Generation                |
| NA12878-I38_L002         | Undefined | 4016146330  | FASTQ Generation                |
| NA12878-I69_L002         | Undefined | 3083704409  | FASTQ Generation                |
| NA12878-I68_L002         | Undefined | 2401722163  | FASTQ Generation                |
| NA12878-I52_L001         | Undefined | 3214369171  | FASTQ Generation                |
| NA12878-I53_L001         | Undefined | 3480342046  | FASTQ Generation                |
| NA12878-I1_L001          | Undefined | 3191184331  | FASTQ Generation                |
| NA12878-I33_L002         | Undefined | 3471775533  | FASTQ Generation                |
| NA12878-I39_L001         | Undefined | 3588737527  | FASTQ Generation                |
| NA12878-I3_L002          | Undefined | 3443809678  | FASTQ Generation                |
| NA12878-I3_L001          | Undefined | 3506095262  | FASTQ Generation                |
| NA12878-I63_L002         | Undefined | 2592179441  | FASTQ Generation                |
| NA12878-I58_L002         | Undefined | 4096988784  | FASTQ Generation                |
| NA12878-I63_L001         | Undefined | 2637306453  | FASTQ Generation                |
| NA12878-I58_L001         | Undefined | 4166358915  | FASTQ Generation                |
| NA12878-I52_L002         | Undefined | 3168690916  | FASTQ Generation                |
| NA12878-I1_L002          | Undefined | 3132985241  | FASTQ Generation                |
| NA12878-I53_L002         | Undefined | 3416347761  | FASTQ Generation                |
| NA12878-I19_L001         | Undefined | 3957041101  | FASTQ Generation                |
| NA12878-I6_L001          | Undefined | 3391399053  | FASTQ Generation                |
| NA12878-I6_L002          | Undefined | 3331911357  | FASTQ Generation                |
| NA12878-I19_L002         | Undefined | 3888583731  | FASTQ Generation                |
| NA12878-I39_L002         | Undefined | 3528621362  | FASTQ Generation                |
| NA12878-I22_L001         | Undefined | 4761206940  | FASTQ Generation                |
| NA12878-I94_L001         | Undefined | 2754680245  | FASTQ Generation                |
| NA12878-I62_L002         | Undefined | 2640117069  | FASTQ Generation                |
| NA12878-I57_L002         | Undefined | 4137590770  | FASTQ Generation                |
| NA12878-I57_L001         | Undefined | 4206859957  | FASTQ Generation                |
| NA12878-I62_L001         | Undefined | 2686027035  | FASTQ Generation                |
| NA12878-I59_L001         | Undefined | 3783044468  | FASTQ Generation                |
| NA12878-I79_L002         | Undefined | 2840663867  | FASTQ Generation                |
| NA12878-I22_L002         | Undefined | 4684041831  | FASTQ Generation                |
| NA12878-I79_L001         | Undefined | 2889704220  | FASTQ Generation                |
| NA12878-I95_L001         | Undefined | 2267562351  | FASTQ Generation                |
| NA12878-I28_L001         | Undefined | 3041447119  | FASTQ Generation                |
| NA12878-I16_L002         | Undefined | 3292494431  | FASTQ Generation                |
| NA12878-I89_L002         | Undefined | 2434115153  | FASTQ Generation                |
| NA12878-I43_L002         | Undefined | 3246057419  | FASTQ Generation                |
| NA12878-I16_L001         | Undefined | 3339361050  | FASTQ Generation                |
| NA12878-I43_L001         | Undefined | 3304536382  | FASTQ Generation                |
| NA12878-I89_L001         | Undefined | 2479438313  | FASTQ Generation                |
| NA12878-I9_L001          | Undefined | 4760896599  | FASTQ Generation                |
| NA12878-I84_L001         | Undefined | 3868301008  | FASTQ Generation                |
| NA12878-I94_L002         | Undefined | 2707270472  | FASTQ Generation                |
| NA12878-I95_L002         | Undefined | 2224678696  | FASTQ Generation                |
| NA12878-I28_L002         | Undefined | 3007510100  | FASTQ Generation                |
| NA12878-I27_L001         | Undefined | 2859100398  | FASTQ Generation                |
| NA12878-I65_L001         | Undefined | 2360451184  | FASTQ Generation                |
| NA12878-I9_L002          | Undefined | 4680728081  | FASTQ Generation                |
| NA12878-I59_L002         | Undefined | 3713797541  | FASTQ Generation                |
| NA12878-I84_L002         | Undefined | 3806501192  | FASTQ Generation                |
| NA12878-I27_L002         | Undefined | 2816327880  | FASTQ Generation                |
| NA12878-I65_L002         | Undefined | 2323119320  | FASTQ Generation                |
| NA12878-I66_L002         | Undefined | 2792918038  | FASTQ Generation                |
| NA12878-I55_L002         | Undefined | 3064208220  | FASTQ Generation                |
| NA12878-I36_L002         | Undefined | 4155743658  | FASTQ Generation                |
| NA12878-I66_L001         | Undefined | 2837871038  | FASTQ Generation                |
| NA12878-I55_L001         | Undefined | 3120683270  | FASTQ Generation                |
| NA12878-I36_L001         | Undefined | 4219946387  | FASTQ Generation                |
| NA12878-I81_L001         | Undefined | 3352618253  | FASTQ Generation                |
| NA12878-I46_L001         | Undefined | 4043290222  | FASTQ Generation                |
| NA12878-I83_L001         | Undefined | 3278163443  | FASTQ Generation                |
| NA12878-I81_L002         | Undefined | 3297908512  | FASTQ Generation                |
| NA12878-I83_L002         | Undefined | 3217615514  | FASTQ Generation                |
| NA12878-I46_L002         | Undefined | 3975332242  | FASTQ Generation                |
| NA12878-I4_L002          | Undefined | 2657480810  | FASTQ Generation                |
| NA12878-I10_L002         | Undefined | 4616959152  | FASTQ Generation                |
| NA12878-I50_L001         | Undefined | 3121452283  | FASTQ Generation                |
| NA12878-I10_L001         | Undefined | 4698066155  | FASTQ Generation                |
| NA12878-I4_L001          | Undefined | 2698170166  | FASTQ Generation                |
| NA12878-I50_L002         | Undefined | 3061460073  | FASTQ Generation                |
| NA12878-I23_L002         | Undefined | 2777539007  | FASTQ Generation                |
| NA12878-I23_L001         | Undefined | 2837699927  | FASTQ Generation                |
| NA12878-I45_L002         | Undefined | 3563213012  | FASTQ Generation                |
| NA12878-I45_L001         | Undefined | 3621319764  | FASTQ Generation                |
| NA12878-I75_L001         | Undefined | 3117341589  | FASTQ Generation                |
| NA12878-I75_L002         | Undefined | 3066328990  | FASTQ Generation                |
| NA12878-I14_L001         | Undefined | 4046659386  | FASTQ Generation                |
| NA12878-I88_L001         | Undefined | 2344920533  | FASTQ Generation                |
| NA12878-I49_L001         | Undefined | 3472980138  | FASTQ Generation                |
| NA12878-I70_L002         | Undefined | 3280083714  | FASTQ Generation                |
| NA12878-I70_L001         | Undefined | 3331074382  | FASTQ Generation                |
| NA12878-I14_L002         | Undefined | 3974780842  | FASTQ Generation                |
| NA12878-I60_L001         | Undefined | 4346140334  | FASTQ Generation                |
| NA12878-I49_L002         | Undefined | 3407734044  | FASTQ Generation                |
| NA12878-I88_L002         | Undefined | 2312767180  | FASTQ Generation                |
| NA12878-I60_L002         | Undefined | 4278157347  | FASTQ Generation                |
| NA12878-R8               | Undefined | 45799019800 | Whole Genome Sequencing         |
| NA12878-R6               | Undefined | 50105768169 | Whole Genome Sequencing         |
| NA12878-R7               | Undefined | 55911719831 | Whole Genome Sequencing         |
| NA12878-R3               | Undefined | 59241988562 | Whole Genome Sequencing         |
| NA12878-R5               | Undefined | 63937184754 | Whole Genome Sequencing         |
| NA12878-R4               | Undefined | 65007812734 | Whole Genome Sequencing         |
| NA12878-R1               | Undefined | 66225618517 | Whole Genome Sequencing         |
| NA12878-R2               | Undefined | 69753821551 | Whole Genome Sequencing         |
| NA12878-R1S1vcf-38337470 | Undefined | 74470807    | Variant Calling Assessment Tool |
| NA12878-R2S1vcf-38347407 | Undefined | 74935322    | Variant Calling Assessment Tool |
| NA12878-R7S1vcf-38332429 | Undefined | 72823358    | Variant Calling Assessment Tool |
| NA12878-R3S1vcf-38334439 | Undefined | 73240361    | Variant Calling Assessment Tool |
| NA12878-R5S1vcf-38332433 | Undefined | 74204818    | Variant Calling Assessment Tool |
| NA12878-R4S1vcf-38337469 | Undefined | 74321860    | Variant Calling Assessment Tool |
| NA12878-R6S1vcf-38345414 | Undefined | 71931600    | Variant Calling Assessment Tool |
| NA12878-R8S1vcf-38345413 | Undefined | 71079147    | Variant Calling Assessment Tool |
| NA12878-R8               | Undefined | 45907338218 | Whole Genome Sequencing         |
| NA12878-R7               | Undefined | 56061546943 | Whole Genome Sequencing         |
| NA12878-R6               | Undefined | 50244728842 | Whole Genome Sequencing         |
| NA12878-R4               | Undefined | 65196853135 | Whole Genome Sequencing         |
| NA12878-R5               | Undefined | 64130024737 | Whole Genome Sequencing         |
| NA12878-R2               | Undefined | 69981057129 | Whole Genome Sequencing         |
| NA12878-R1               | Undefined | 66430007075 | Whole Genome Sequencing         |
| NA12878-R3               | Undefined | 59407154231 | Whole Genome Sequencing         |
| NA12878-I77_L001         | Undefined | 3084881895  | FASTQ Generation                |
| NA12878-I11_L001         | Undefined | 3691783167  | FASTQ Generation                |
| NA12878-I15_L002         | Undefined | 4106873931  | FASTQ Generation                |
| NA12878-I5_L001          | Undefined | 3639561658  | FASTQ Generation                |
| NA12878-I92_L001         | Undefined | 2155352183  | FASTQ Generation                |
| NA12878-I15_L001         | Undefined | 4178689004  | FASTQ Generation                |
| NA12878-I21_L001         | Undefined | 4226684511  | FASTQ Generation                |
| NA12878-I26_L002         | Undefined | 3698199861  | FASTQ Generation                |
| NA12878-I77_L002         | Undefined | 3036350106  | FASTQ Generation                |
| NA12878-I11_L002         | Undefined | 3620890660  | FASTQ Generation                |
| NA12878-I26_L001         | Undefined | 3758050376  | FASTQ Generation                |
| NA12878-I2_L001          | Undefined | 3231688300  | FASTQ Generation                |
| NA12878-I74_L002         | Undefined | 3048813601  | FASTQ Generation                |
| NA12878-I74_L001         | Undefined | 3102267532  | FASTQ Generation                |
| NA12878-I35_L002         | Undefined | 3259191028  | FASTQ Generation                |
| NA12878-I35_L001         | Undefined | 3317208579  | FASTQ Generation                |
+--------------------------+-----------+-------------+---------------------------------+

Drilling down into a data set

Get details about one data set.

This example is from the VCAT app:

$ bs -c v2cli_prod get dataset -i ds.f45e4fcccbce4fb18dd91bdad7dcb272
+---------------------------------------------------+----------------------------------------------------------------------------------------+
| Id                                                | ds.f45e4fcccbce4fb18dd91bdad7dcb272                                                    |
| Name                                              | NA12878-R1S1vcf-38337470                                                               |
| AppSession.Id                                     | 42463886                                                                               |
| AppSession.Name                                   | NA12878-R1_S1.vcf.gz_2                                                                 |
| AppSession.Application.AppFamilySlug              | basespace-labs.variant-calling-assessment-tool                                         |
| AppSession.Application.AppVersionSlug             | basespace-labs.variant-calling-assessment-tool.3.0.0                                   |
| AppSession.Application.Id                         | 2106105                                                                                |
| AppSession.Application.VersionNumber              | 3.0.0                                                                                  |
| AppSession.Application.HomepageUri                | http://www.illumina.com                                                                |
| AppSession.Application.ShortDescription           | The Variant Calling Assessment Tool (VCAT) enables                                     |
|                                                   | the comparison of variant call sets using VCF files                                    |
|                                                   | as input.                                                                              |
| AppSession.Application.LongDescription            |                                                                                        |
| AppSession.Application.Category                   | Native                                                                                 |
| AppSession.Application.UserOwnedBy.Id             |                                                                                        |
| AppSession.Application.UserOwnedBy.Name           |                                                                                        |
| AppSession.Application.UserOwnedBy.GravatarURL    |                                                                                        |
| AppSession.Application.UserOwnedBy.DateLastActive |                                                                                        |
| AppSession.Application.UserOwnedBy.DateCreated    |                                                                                        |
| AppSession.Application.Name                       | Variant Calling Assessment Tool                                                        |
| AppSession.Application.CompanyName                | BaseSpace Labs                                                                         |
| AppSession.ExecutionStatus                        | Complete                                                                               |
| AppSession.QcStatus                               | Undefined                                                                              |
| AppSession.DeliveryStatus                         | None                                                                                   |
| AppSession.UserCreatedBy.Id                       | 9319322                                                                                |
| AppSession.UserCreatedBy.Name                     | Illumina Public Data                                                                   |
| AppSession.UserCreatedBy.GravatarURL              | https://secure.gravatar.com/avatar/c028aa9f7bb49e5c99efd2c6a329d8d6.jpg?s=20&d=mm&r=PG |
| AppSession.UserCreatedBy.DateLastActive           |                                                                                        |
| AppSession.UserCreatedBy.DateCreated              | 2016-10-25T17:38:36.0000000                                                            |
| AppSession.StatusSummary                          | Application completed successfully                                                     |
| AppSession.TotalSize                              | 0                                                                                      |
| Project.Name                                      | NovaSeq: TruSeq Nano 550 (Replicates of NA12878)                                       |
| Project.Id                                        | 36080093                                                                               |
| Project.Description                               | The TruSeq Nano 550 library was prepared using Human DNA from Coriell Sample NA12878.  |
|                                                   | The 96-plex pool was sequenced on a NovaSeq with S2 Flowcell. BaseSpace was used to    |
|                                                   | combine groups of 12 samples at a time into 8 samples of varying depth.  Secondary     |
|                                                   | analysis was run using the Whole Genome Sequencing v5 and Variant Calling Assessment   |
|                                                   | Tool v3 BaseSpace Apps.                                                                |
| Project.TotalSize                                 | 2233311909088                                                                          |
| UserOwnedBy.Id                                    | 9319322                                                                                |
| UserOwnedBy.Name                                  | Illumina Public Data                                                                   |
| UserOwnedBy.GravatarURL                           | https://secure.gravatar.com/avatar/c028aa9f7bb49e5c99efd2c6a329d8d6.jpg?s=20&d=mm&r=PG |
| UserOwnedBy.DateLastActive                        |                                                                                        |
| UserOwnedBy.DateCreated                           | 2016-10-25T17:38:36.0000000                                                            |
| DataSetType.Id                                    | common.files                                                                           |
| DataSetType.Name                                  | Common Files                                                                           |
| QcStatus                                          | Undefined                                                                              |
| QcStatusSummary                                   | No thresholds were evaluated                                                           |
| UploadStatus                                      | Completed                                                                              |
| UploadStatusSummary                               |                                                                                        |
| ValidationStatus                                  | Passed                                                                                 |
| TotalSize                                         | 74470807                                                                               |
+---------------------------------------------------+----------------------------------------------------------------------------------------+

Get dataset attributes

This example is a FASTQ app:

$ bs list attributes dataset -i ds.2f5b56dddc0440858943246ba4ac9d11
+---------------------+---------------+
|        Name         |     Value     |
+---------------------+---------------+
| TotalReadsPF        | 4.1119628e+07 |
| MaxLengthIndexRead1 | 8             |
| MaxLengthRead1      | 151           |
| MaxLengthRead2      | 151           |
| IsPairedEnd         | true          |
| TotalClustersPF     | 2.0559814e+07 |
| TotalClustersRaw    | 2.6711606e+07 |
| TotalReadsRaw       | 5.3423212e+07 |
| MaxLengthIndexRead2 | 8             |
+---------------------+---------------+

Get file contents for a dataset

This is a VCAT example:

$ bs contents dataset -i ds.f45e4fcccbce4fb18dd91bdad7dcb272
+------------+-----------------------------------------------------------------------------------------+
|     Id     |                                        FilePath                                         |
+------------+-----------------------------------------------------------------------------------------+
| 7240583239 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.vcf.gz.tbi   |
| 7240583238 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.vcf.gz       |
| 7240583237 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.summary.csv  |
| 7240583236 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.metrics.json |
| 7240583235 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.extended.csv |
| 7240583234 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.counts.json  |
| 7240583233 | happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.counts.csv   |
| 7240583232 | report.log                                                                              |
| 7240583231 | report.json                                                                             |
+------------+-----------------------------------------------------------------------------------------+


Download subset of files (by extension) from a dataset as a tgz:

# will download into file /tmp/vcat.tar.gz
$ bs download dataset -i ds.2f5b56dddc0440858943246ba4ac9d11 --extension=json -o /tmp/vcat
NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.metrics.json  27.44 KB / 27.44 KB [============] 100.00% 348.12 KB/s 0s
happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.metrics.json
NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.counts.json  5.02 KB / 5.02 KB [================] 100.00% 22.04 MB/s 0s
happy/NA12878-R1_S1-vcf-38337470__NA12878-Platinum-Genomes-v2016-1-0-hg38-.counts.json
report.json  2.53 KB / 2.53 KB [=====================================================================================] 100.00% 13.41 MB/s 0s
report.json
NA12878-R1S1vcf-38337470.ds.f45e4fcccbce4fb18dd91bdad7dcb272.json  2.71 KB / 2.71 KB [===============================] 100.00% 61.58 MB/s 0s
NA12878-R1S1vcf-38337470.ds.f45e4fcccbce4fb18dd91bdad7dcb272.json

Setting lane QC thresholds

Authenticate with the appropriate scopes into a config called "laneqc"

We will refer to this in future commands.

$ ./bs auth --scope="READ GLOBAL","CREATE GLOBAL","CONFIGURE QC" -c laneqc
Please go to this URL to authenticate:  https://basespace.illumina.com/oauth/device?code=HrACj
Created config file  /Users/basespaceuser/.basespace/laneqc.cfg
Welcome, BSSH.V2 TestUser

Look at lane QC thresholds to confirm they are blank:

$ bs -c laneqc lane threshold export
Name,Group,Operator,ThresholdValues

Create a csv file to define the QC thresholds and set the lane QC thresholds using that file:

$ cat > /tmp/thresholds.txt                                       
Name,Group,Operator,ThresholdValues                                   
PercentGtQ30,SequencingRead1,GreaterThanOrEqual,50                    
PercentGtQ30,SequencingRead2,GreaterThanOrEqual,40                    
$ bs -c laneqc lane threshold import -f /tmp/thresholds.txt          
# should finish without errors!                                      

View lane QC thresholds:

$ bs -c laneqc lane threshold export                                 
Name,Group,Operator,ThresholdValues                                   
PercentGtQ30,SequencingRead1,GreaterThanOrEqual,50                    
PercentGtQ30,SequencingRead2,GreaterThanOrEqual,40                    

Clear lane QC thresholds to remove them and view to make sure they have been cleared:

$ bs -c laneqc lane threshold clear                                  
$ ./bs -c laneqc lane threshold export                               
Name,Group,Operator,ThresholdValues                                   

Creating a biosample and uploading FASTQ data against it

Biosample Creation

# warning! if your project does not already exist it will be implicitly created                                                    
$ bs create biosample -n "MyBioSample" -p "MyProject"                

Note that there are quite a few optional metadata parameters for biosamples. These are primarily designed to help high-throughput labs classify and display biosamples:

$ bs create biosample --help
(snip)
    BioSample Options:
      -n, --name=                                  Name of the BioSample
      -p, --project=                               Name of the project where FastQs will be stored. Created if not found.
          --container-name=                        Name of container
          --container-position=                    Position within the container
          --analysis-workflow=                     Name of the analysis to schedule
          --prep-request=                          Name of the lab workflow that LIMS should perform
          --required-yield=                        Required yield in Gbp that is needed before launching analysis (required if --prep-request is provided)
          --metadata=                              Key/Value metadata properties to set on the BioSample
          --delivery-mode=[Deliver|Do Not Deliver] Intial delivery mode
(snip)


You can preview biosample creation (--preview), to validate that the data provided is correct.

$ bs create biosample -n "MyBioSample" -p "MyProject" --preview      
ERROR:  * * * Error in BioSample Name: BioSample 'MyBioSample' already exists and cannot be imported  * * *                                  

To attach a new analysis workflow to an existing biosample, use the --allow-existing option.

FASTQ upload

There are two options to associate uploaded FASTQ files with a biosample:

  • Upload files that match the biosample name
  • Force the upload to attach FASTQs to the specified biosample, regardless of their name

Upload FASTQ files that match the biosample name

$ ls                                                                 
MyBioSample_S1_L001_R1_001.fastq.gz                               
MyBioSample_S1_L001_R2_001.fastq.gz                               
# note that you need a project ID here, not a project name as you did when you created the biosample!                                       
$ bs upload dataset -p 27943921                                      
MyBioSample_S1_L001_R1_001.fastq.gz                               
MyBioSample_S1_L001_R2_001.fastq.gz                               
Sample(MyBioSample)  [1/1 ] Upload started                            
Sample(MyBioSample) Metadata complete. Waiting for upload             completion...                                                         
Sample(MyBioSample) Upload complete                                   
# note that datasets and created asynchronously and there can be a delay
$ bs list dataset --input-biosample="MyBioSample"  
+-------------+-------------------------------------+--------------+---------------------+
|    Name     |                 Id                  | Project.Name |   DataSetType.Id    |
+-------------+-------------------------------------+--------------+---------------------+
| MyBioSample | ds.94f7e9663e86473c8582dcf85a830195 | MyProject    | illumina.fastq.v1.8 |
+-------------+-------------------------------------+--------------+---------------------+

Force the upload to attach FASTQS to the specified biosample, regardless of their name

$ ls
valid_S1_L001_R1_001.fastq.gz   valid_S1_L001_R2_001.fastq.gz
# note that you need a project ID here, not a project name as you did when you created the biosample!
$ bs upload dataset --biosample-name="MyBioSample" -p 27943921 valid_S1_L001_R1_001.fastq.gz valid_S1_L001_R2_001.fastq.gz
Sample(MyBioSample) [1/1] Upload started
Sample(MyBioSample) Metadata complete. Waiting for upload completion...
Sample(MyBioSample) Upload complete
$ /tmp/BSCLI/amd64-darwin/bs list dataset --input-biosample="MyBioSample"
+-------------+-------------------------------------+--------------+---------------------+
|    Name     |                 Id                  | Project.Name |   DataSetType.Id    |
+-------------+-------------------------------------+--------------+---------------------+
| MyBioSample | ds.94f7e9663e86473c8582dcf85a830195 | MyProject    | illumina.fastq.v1.8 |
| MyBioSample | ds.64706f7d2e504e1c9495c00c468d6640 | MyProject    | illumina.fastq.v1.8 |
+-------------+-------------------------------------+--------------+---------------------+

Note that even though the dataset has a name to match the biosample, the files within retain their original names:

$ bs dataset contents -i ds.94f7e9663e86473c8582dcf85a830195
+------------+-------------------------------------+
|     Id     |              FilePath               |
+------------+-------------------------------------+
| 8652306587 | MyBioSample_S1_L001_R1_001.fastq.gz |
| 8652306586 | MyBioSample_S1_L001_R2_001.fastq.gz |
+------------+-------------------------------------+
$ bs dataset contents -i ds.64706f7d2e504e1c9495c00c468d6640
+------------+-------------------------------+
|     Id     |           FilePath            |
+------------+-------------------------------+
| 8652572270 | valid_S1_L001_R2_001.fastq.gz |
| 8652572269 | valid_S1_L001_R1_001.fastq.gz |
+------------+-------------------------------+

Configure Automated Workflow

There are two prerequisites to creating an automated workflow: - Acquire a token with MANAGE APPLICATIONS scope. If you don't have the token, the following error message appears: BASESPACE.COMMON.CANNOT_CREATE_WORKFLOW: Cannot create workflow with the current token scope

  • Create an appsession to use as a template for the workflow. Use the same settings you want to include in the automated workflow.

Get a token

Get the MANAGE APPLICATIONS token to create and work with workflows:

$ bs auth -c emea --force --api-server https://api.emea.illumina.com/ --scopes "READ GLOBAL","CREATE GLOBAL","BROWSE GLOBAL","MANAGE APPLICATIONS"

Create a Workflow

$ bs -c cloud-manageapps workflow create -n TestWorkflow -d CLICreated --application-id=2039037 --appsession-id=41060211
3978975

In this example, the application and appsession are based on the WGS5.0.0 app.

The value returned is the ID of the workflow. You can see it by doing:

$ bs -c cloud-manageapps list applications --category=workflow
+--------------+---------+---------------+
|     Name     |   Id    | VersionNumber |
+--------------+---------+---------------+
| TestWorkflow | 3978975 | 1.0.0         |
+--------------+---------+---------------+

Set Dependencies

Create a biosample yield dependency:

$ bs -c cloud-manageapps workflow dependency add biosample-yield --chooser-id=sample-id --can-use-primary-biosample -i 3978975</pre>

Create an app completion dependency:

$ bs -c cloud-manageapps workflow dependency add app-completion --application-id illumina-lab-services.genotyping-vcf-uploader.1.0.0 -i 3978975 --chooser-id=array-vcf-file --qc-pass --file-selector='.*\\.vcf\\.gz$|.*\\.vcf$'</pre>

Review:

$ bs -c cloud-manageapps workflow dependency export -i 3978975
[
  {
    "Type": "BioSampleYield",
    "Attributes": {
      "BioSampleChooserId": "sample-id",
      "CanUsePrimaryBioSample": false,
      "Label": "",
      "LibraryPrepId": "",
      "MixLibraryTypesAllowed": false
    },
    "Dependencies": null
  },
  {
    "Type": "AppCompletion",
    "Attributes": {
      "ApplicationId": "illumina-lab-services.genotyping-vcf-uploader.1.0.0",
      "CanUsePrimaryResource": false,
      "ColumnId": "",
      "Label": "",
      "RequireQcPass": true,
      "ResourceChooserId": "array-vcf-file"
    },
    "Dependencies": null
  }
]

Set QC Thresholds

In this example, the thresholds are configured in the following csv file:

/tmp/qcthresholds.csv

Name

DatasetTypeId

Operator

ThresholdValues

illumina_isaac_v5.autosome_callability

illumina.isaac.v5

GreaterThanOrEqual

95

illumina_isaac_v5.autosome_coverage_at_10x

illumina.isaac.v5

GreaterThanOrEqual

98

illumina_isaac_v5.autosome_coverage_at_1x

illumina.isaac.v5

GreaterThanOrEqual

99.49

illumina_isaac_v5.autosome_exon_callability

illumina.isaac.v5

GreaterThanOrEqual

97

illumina_isaac_v5.autosome_exon_coverage_at_10x

illumina.isaac.v5

GreaterThanOrEqual

98.5

illumina_isaac_v5.autosome_exon_coverage_at_1x

illumina.isaac.v5

GreaterThanOrEqual

99.29

illumina_isaac_v5.autosome_mean_coverage

illumina.isaac.v5

GreaterThanOrEqual

30

illumina_isaac_v5.cnvs

illumina.isaac.v5

LessThanOrEqual

300

illumina_isaac_v5.contamination

illumina.isaac.v5

LessThanOrEqual

5

illumina_isaac_v5.fragment_length_median

illumina.isaac.v5

GreaterThanOrEqual

420

illumina_isaac_v5.frameshift_deletions

illumina.isaac.v5

GreaterThanOrEqual

0

illumina_isaac_v5.indel_het_to_hom_ratio

illumina.isaac.v5

LessThanOrEqual

2.5

illumina_isaac_v5.mapq_more_than_10_autosome_coverage_at_15x

illumina.isaac.v5

GreaterThanOrEqual

95

illumina_isaac_v5.mapq_more_than_10_autosome_exon_coverage_at_15x

illumina.isaac.v5

GreaterThanOrEqual

95

illumina_isaac_v5.mismatch_rate_read_1

illumina.isaac.v5

LessThanOrEqual

1

illumina_isaac_v5.mismatch_rate_read_2

illumina.isaac.v5

LessThanOrEqual

2.3

illumina_isaac_v5.percent_aligned_reads

illumina.isaac.v5

GreaterThanOrEqual

92

illumina_isaac_v5.percent_at_dropout

illumina.isaac.v5

LessThanOrEqual

2.43

illumina_isaac_v5.percent_gc_dropout

illumina.isaac.v5

LessThanOrEqual

2.5

illumina_isaac_v5.percent_q30_bases

illumina.isaac.v5

GreaterThanOrEqual

80

illumina_isaac_v5.percent_q30_bases_read_2

illumina.isaac.v5

GreaterThanOrEqual

77

illumina_isaac_v5.percent_read_pairs_aligned_to_different_chromosomes

illumina.isaac.v5

LessThanOrEqual

1.5

illumina_isaac_v5.q30_bases_excluding_clipped_and_duplicate_read_bases

illumina.isaac.v5

GreaterThanOrEqual

9e+10

illumina_isaac_v5.read_enrichment_at_80percent_gc

illumina.isaac.v5

GreaterThanOrEqual

0.8

illumina_isaac_v5.snv_het_to_hom_ratio

illumina.isaac.v5

LessThanOrEqual

2.05

illumina_isaac_v5.total_pf_bases

illumina.isaac.v5

GreaterThanOrEqual

1e+11

illumina_isaac_v5.array_concordance

illumina.isaac.v5

GreaterThanOrEqual

99.3

illumina_isaac_v5.array_concordance_usage

illumina.isaac.v5

GreaterThanOrEqual

95

Do this:

$ bs -c cloud-manageapps workflow threshold import -f /tmp/qcthresholds.csv -i 3978975

Accession Biosample

To create a new instance of your workflow, create a biosample with that workflow. Note that you need to use the project name not the ID here - this is to match the manifest import mechanism.

$ bs -c cloud-manageapps biosample import -p "MyProject" -n "MyBiosample" --workflow-name "TestWorkflow"

Inspect the Biosamples you've just created

$ bs list biosamples

Find the appsession that's been created as your workflow

Setting different fields here shows you extra information about the status. Note that you need to use the biosample ID and not the name here.

$ bs -c cloud-manageapps appsession list --input-biosamples=$BIOSAMPLEID -F Id -F Status -F StatusSummary

Upload Fastq files against that biosample

Uploading data against your new biosample can be carried out as listed in a previous example. This will register yield against this biosample that can trigger an app launch if the workflow has a yield dependency.