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IGF-HPC-Airf...
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airflow_var
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var.json

var.json 11 KB
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  1. {
    2. 

  2.   "celery_flower_base_url": "http://igf-lims.cc.ic.ac.uk:5555",
    3. 

  3.   "redis_conn_file": "/rds/general/user/igf/home/data2/airflow_test/secrets/redis_conn.json",
    4. 

  4.   "hpc_host": "login.hpc.ic.ac.uk",
    5. 

  5.   "hpc_user": "igf",
    6. 

  6.   "igf_lims_ssh_key_file": "/SSH/id_rsa_airflow",
    7. 

  7.   "hpc_ssh_key_file": "/home/igf/.ssh/id_rsa",
    8. 

  8.   "hpc_max_workers_per_queue": 10,
    9. 

  9.   "hpc_max_total_workers": 40,
    10. 

  10.   "crick_ftp_seqrun_hostname": "hermes.crick.ac.uk",
    11. 

  11.   "crick_ftp_config_file_orwell": "/home/igf/igf_code/airflow/secret/crick_ftp_config.json",
    12. 

  12.   "crick_ftp_config_file_wells": "/rds/general/user/igf/home/data2/airflow_test/secrets/crick_ftp_config.json",
    13. 

  13.   "crick_ftp_base_path": "/users/dattaa/runs",
    14. 

  14.   "confluence_config": "/rds/general/user/igf/home/secret_keys/confluence_private_api_key.json",
    15. 

  15.   "wiki_publication_page_id": 293602542,
    16. 

  16.   "wiki_publication_page_title": "Publications",
    17. 

  17.   "seqrun_base_path": "/home/igf/seqrun/illumina",
    18. 

  18.   "seqrun_server_user": "igf",
    19. 

  19.   "database_config_file": "/rds/general/user/igf/home/secret_keys/dbconfig.json",
    20. 

  20.   "test_database_config_file": "/rds/general/user/igf/home/secret_keys/testdbconfig.json",
    21. 

  21.   "slack_conf": "/rds/general/user/igf/home/secret_keys/slack_config.json",
    22. 

  22.   "analysis_slack_conf": "/rds/general/user/igf/home/secret_keys/slack_config2.json",
    23. 

  23.   "asana_conf": "/rds/general/user/igf/home/secret_keys/asana_conf.json",
    24. 

  24.   "asana_demult_project": "381635035883061",
    25. 

  25.   "asana_analysis_project": "744376995776821",
    26. 

  26.   "ms_teams_conf": "/rds/general/user/igf/home/secret_keys/team_de-mult.json",
    27. 

  27.   "analysis_ms_teams_conf": "/rds/general/user/igf/home/secret_keys/team_analysis.json",
    28. 

  28.   "hpc_seqrun_path": "/rds/general/project/genomics-facility-archive-2019/ephemeral/",
    29. 

  29.   "interop_dumptext_exe": "/rds/general/user/igf/home/anaconda3/envs/interop/bin/interop_dumptext",
    30. 

  30.   "interop_notebook_image_path": "/project/tgu/resources/pipeline_resource/singularity_images/interop/interop-notebook-image_v3.sif",
    31. 

  31.   "interop_notebook_template": "/project/tgu/software/interop-notebook-image/templates/interop_report_v0.0.2.ipynb",
    32. 

  32.   "seqrun_ml_notebook_template": "/project/tgu/software/interop-notebook-image/templates/seqrun_ml_v0.0.1.ipynb",
    33. 

  33.   "seqrun_training_data_csv": "/project/tgu/resources/pipeline_resource/seqrun_ml/seqrun_training_data.csv",
    34. 

  34.   "box_dir_prefix_for_seqrun_report": "De-multiplexing_reports",
    35. 

  35.   "box_username": "igf@imperial.ac.uk",
    36. 

  36.   "box_config_file": "/rds/general/user/igf/home/secret_keys/boxconfig.json",
    37. 

  37.   "bcl2fastq_image_path": "/project/tgu/resources/pipeline_resource/singularity_images/igf-demultiplexing-image/igf-demultiplexing-image_v0.0.1.sif",
    38. 

  38.   "pandoc_image_path": "/project/tgu/resources/pipeline_resource/singularity_images/pandoc/pandoc.sif",
    39. 

  39.   "singlecell_barcode_json": "/project/tgu/data2/airflow_test/github/data-management-python/data/singlecell_data/chromium-shared-sample-indexes-plate_20180301.json",
    40. 

  40.   "singlecell_dual_barcode_json": "/project/tgu/data2/airflow_test/github/data-management-python/data/singlecell_data/chromium_dual_indexes_plate_TT_NT_20210209.json",
    41. 

  41.   "samplesheet_validation_json": "/project/tgu/data2/airflow_test/github/data-management-python/data/validation_schema/samplesheet_validation.json",
    42. 

  42.   "seqrun_server": "orwell.hh.med.ic.ac.uk",
    43. 

  43.   "orwell_server_hostname": "orwell.hh.med.ic.ac.uk",
    44. 

  44.   "woolf_server_hostname": "woolf.med.ic.ac.uk",
    45. 

  45.   "eliot_server_hostname": "eliot.med.ic.ac.uk",
    46. 

  46.   "igf_lims_server_hostname": "igf-lims.cc.ic.ac.uk",
    47. 

  47.   "tenx_single_cell_immune_profiling_feature_types": {"gene_expression": "", "vdj-t": "", "vdj-b": "", "antibody_capture": "", "antigen_capture": "", "crisper_guide_capture": ""},
    48. 

  48.   "analysis_dag_list": {"dag9_tenx_single_cell_immune_profiling": "", "dag12_nextflow_chipseq_pipeline": "", "dag10_nextflow_atacseq_pipeline": ""},
    49. 

  49.   "analysis_lookup_dir": "/project/tgu/data2/pipeline_control/analysis_designs",
    50. 

  50.   "analysis_triger_file": "/project/tgu/data2/pipeline_control/analysis_trigger.csv",
    51. 

  51.   "scanpy_single_sample_template": "/project/tgu/software/scanpy-notebook-image/templates/scanpy_single_sample_analysis_v0.0.6.ipynb",
    52. 

  52.   "scvelo_single_sample_template": "/project/tgu/software/scanpy-notebook-image/templates/scvelo_basic_single_sample_v0.0.1.ipynb",
    53. 

  53.   "scanpy_notebook_image": "/project/tgu/resources/pipeline_resource/singularity_images/scanpy-notebook-image/scanpy-notebook-image_v0.0.4.sif",
    54. 

  54.   "scirpy_single_sample_template": "/project/tgu/software/scirpy-notebook-image/templates/scirpy_basic_v0.0.4.ipynb",
    55. 

  55.   "scirpy_notebook_image": "/project/tgu/resources/pipeline_resource/singularity_images/scirpy/scirpy-notebook-image_v0.0.2.sif",
    56. 

  56.   "seurat_single_sample_template": "/project/tgu/software/seurat-notebook-image/templates/seurat_basic_v0.0.2.ipynb",
    57. 

  57.   "seurat_notebook_image": "/project/tgu/resources/pipeline_resource/singularity_images/seurat/seurat_release_v0.0.1.sif",
    58. 

  58.   "irods_exe_dir": "/apps/irods/4.2.0/irods/iRODS/clients/icommands/bin",
    59. 

  59.   "ftp_hostname": "eliot.med.ic.ac.uk",
    60. 

  60.   "ftp_username": "igf",
    61. 

  61.   "ftp_project_path": "/www/html/report/project",
    62. 

  62.   "all_cell_marker_list": "/project/tgu/resources/pipeline_resource/cell_markers/PangaloDB/PanglaoDB_markers_27_Mar_2020.tsv",
    63. 

  63.   "cellranger_exe": "/project/tgu/resources/cellranger-6.1.2/bin/cellranger",
    64. 

  64.   "base_result_dir": "/project/tgu/data2/results",
    65. 

  65.   "cellranger_job_timeout": 259200,
    66. 

  66.   "cutadapt_singularity_image": "/project/tgu/resources/pipeline_resource/singularity_images/cutadapt/cutadapt_v3.1.sif",
    67. 

  67.   "multiqc_singularity_image": "/project/tgu/resources/pipeline_resource/singularity_images/cutadapt/cutadapt_v3.1.sif",
    68. 

  68.   "multiqc_template_file": "/project/tgu/data2/airflow_test/github/data-management-python/template/multiqc_report/multiqc_config.yaml",
    69. 

  69.   "picard_singularity_image": "/project/tgu/resources/pipeline_resource/singularity_images/picard/picard_v2.23.9.sif",
    70. 

  70.   "samtools_singularity_image": "/project/tgu/resources/pipeline_resource/singularity_images/samtools/htslib_v1.11.sif",
    71. 

  71.   "igenome_base_path": "/project/tgu/resources/pipeline_resource",
    72. 

  72.   "nextflow_template_file": "/project/tgu/data2/airflow_test/github/data-management-python/igf_nextflow/config/nextflow.cfg_template",
    73. 

  73.   "nextflow_exe": "/project/tgu/software/nextflow/nextflow",
    74. 

  74.   "nextflow_singularity_cache_dir": "/project/tgu/resources/pipeline_resource/nextflow_singularity_cachedir",
    75. 

  75.   "seqrun_demult_notebook_template": "/project/tgu/software/interop-notebook-image/templates/demult_report_v0.0.1.ipynb",
    76. 

  76.   "gtf_ref_path": "/project/tgu/resources/pipeline_resource/gene/gtf",
    77. 

  77.   "star_exe": "/project/tgu/software/STAR/bin/STAR",
    78. 

  78.   "star_ref_path": "/project/tgu/resources/pipeline_resource/transcriptome/STAR",
    79. 

  79.   "rsem_exe_dir": "/project/tgu/software/RSEM",
    80. 

  80.   "rsem_ref_path": "/project/tgu/resources/pipeline_resource/transcriptome/rsem",
    81. 

  81.   "ucsc_exe_dir": "/project/tgu/software/ucsc",
    82. 

  82.   "refflat_ref_path": "/project/tgu/resources/pipeline_resource/gene/refFlat",
    83. 

  83.   "ribosomal_interval_ref_path": "/project/tgu/resources/pipeline_resource/intervals/ribosomal",
    84. 

  84.   "cellranger_ref_path": "/project/tgu/resources/pipeline_resource/transcriptome/cellranger",
    85. 

  85.   "hpc_queue_list": {
    86. 

  86.     "hpc_1G": {
    87. 

  87.       "pbs_resource": "-lselect=1:ncpus=1:mem=1gb -lwalltime=12:00:00",
    88. 

  88.       "airflow_queue": "hpc_1G"},
    89. 

  89.     "hpc_1G4t": {
    90. 

  90.       "pbs_resource": "-lselect=1:ncpus=4:mem=1gb -lwalltime=12:00:00",
    91. 

  91.       "airflow_queue": "hpc_1G,hpc_1G4t"},
    92. 

  92.     "hpc_4G": {
    93. 

  93.       "pbs_resource": "-lselect=1:ncpus=1:mem=4gb -lwalltime=12:00:00",
    94. 

  94.       "airflow_queue": "hpc_1G,hpc_4G"},
    95. 

  95.     "hpc_4G12hr": {
    96. 

  96.       "pbs_resource": "-lselect=1:ncpus=1:mem=4gb -lwalltime=12:00:00",
    97. 

  97.       "airflow_queue": "hpc_1G,hpc_4G,hpc_4G12hr"},
    98. 

  98.     "hpc_4G48hr": {
    99. 

  99.       "pbs_resource": "-lselect=1:ncpus=1:mem=4gb -lwalltime=48:00:00",
    100. 

  100.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G12hr,hpc_4G48hr"},
    101. 

  101.     "hpc_4G4t": {
    102. 

  102.       "pbs_resource": "-lselect=1:ncpus=4:mem=4gb -lwalltime=12:00:00",
    103. 

  103.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t"},
    104. 

  104.     "hpc_4G8t": {
    105. 

  105.       "pbs_resource": "-lselect=1:ncpus=8:mem=4gb -lwalltime=12:00:00",
    106. 

  106.       "airflow_queue": "hpc_1G,,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t"},
    107. 

  107.     "hpc_4G16t": {
    108. 

  108.       "pbs_resource": "-lselect=1:ncpus=16:mem=4gb -lwalltime=12:00:00",
    109. 

  109.       "airflow_queue": "hpc_1G,,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t"},
    110. 

  110.     "hpc_8G": {
    111. 

  111.       "pbs_resource": "-lselect=1:ncpus=1:mem=8gb -lwalltime=12:00:00",
    112. 

  112.       "airflow_queue": "hpc_1G,hpc_4G,hpc_8G"},
    113. 

  113.     "hpc_8G4t": {
    114. 

  114.       "pbs_resource": "-lselect=1:ncpus=4:mem=8gb -lwalltime=12:00:00",
    115. 

  115.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_8G,hpc_8G4t"},
    116. 

  116.     "hpc_8G24hr": {
    117. 

  117.         "pbs_resource": "-lselect=1:ncpus=1:mem=8gb -lwalltime=24:00:00",
    118. 

  118.         "airflow_queue": "hpc_1G,hpc_4G,hpc_4G12hr,hpc_8G,hpc_8G24hr"},
    119. 

  119.     "hpc_8G8t": {
    120. 

  120.       "pbs_resource": "-lselect=1:ncpus=8:mem=8gb -lwalltime=12:00:00",
    121. 

  121.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_8G,hpc_8G4t,hpc_8G8t"},
    122. 

  122.     "hpc_8G16t": {
    123. 

  123.       "pbs_resource": "-lselect=1:ncpus=16:mem=8gb -lwalltime=12:00:00",
    124. 

  124.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16t"},
    125. 

  125.     "hpc_16G24hr": {
    126. 

  126.         "pbs_resource": "-lselect=1:ncpus=1:mem=16gb -lwalltime=24:00:00",
    127. 

  127.         "airflow_queue": "hpc_1G,hpc_4G,hpc_4G12hr,hpc_8G,hpc_16G24hr"},
    128. 

  128.     "hpc_16G4t": {
    129. 

  129.       "pbs_resource": "-lselect=1:ncpus=4:mem=16gb -lwalltime=12:00:00",
    130. 

  130.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_8G,hpc_8G4t,hpc_16G4t"},
    131. 

  131.     "hpc_16G8t": {
    132. 

  132.       "pbs_resource": "-lselect=1:ncpus=8:mem=16gb -lwalltime=12:00:00",
    133. 

  133.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_16G4t,hpc_16G8t"},
    134. 

  134.     "hpc_16G16t": {
    135. 

  135.       "pbs_resource": "-lselect=1:ncpus=16:mem=16gb -lwalltime=12:00:00",
    136. 

  136.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t"},
    137. 

  137.     "hpc_32G8t": {
    138. 

  138.       "pbs_resource": "-lselect=1:ncpus=16:mem=32gb -lwalltime=12:00:00",
    139. 

  139.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G8t,hpc_32G8t"},
    140. 

  140.     "hpc_32G16t": {
    141. 

  141.       "pbs_resource": "-lselect=1:ncpus=16:mem=32gb -lwalltime=12:00:00",
    142. 

  142.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16t"},
    143. 

  143.     "hpc_42G16t": {
    144. 

  144.       "pbs_resource": "-lselect=1:ncpus=16:mem=42gb -lwalltime=12:00:00",
    145. 

  145.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16,hpc_42G16t"},
    146. 

  146.     "hpc_64G16t24hr": {
    147. 

  147.       "pbs_resource": "-lselect=1:ncpus=16:mem=64gb -lwalltime=24:00:00",
    148. 

  148.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16,hpc_42G16t,hpc_64G16t24hr"},
    149. 

  149.     "hpc_64G16t72hr": {
    150. 

  150.       "pbs_resource": "-lselect=1:ncpus=16:mem=64gb -lwalltime=72:00:00",
    151. 

  151.       "airflow_queue": "hpc_1G,hpc_1G4t,hpc_4G,hpc_4G4t,hpc_4G8t,hpc_4G16t,hpc_8G,hpc_8G4t,hpc_8G8t,hpc_8G16,hpc_16G4t,hpc_16G8t,hpc_16G16t,hpc_32G16,hpc_42G16t,hpc_64G16t24hr,hpc_64G16t72hr"}
    152. 

  152.    }
    153. 

  153. }
    154.