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    • Z
      zhanglu 最后由 编辑

      在node03上执行
      1.lammps

      cd /home/user/Desktop/rigid
      source /opt/intel/oneapi/setvars.sh
      gpu
      mpirun -np 20 /opt/software/lammps-7Feb2024/src/lmp_oneapi -sf gpu -pk gpu 1 neigh no -in in.rigid
      cpu
      mpirun -np 20 /opt/software/lammps-7Feb2024/src/lmp_oneapi < in.rigid

      1 条回复 最后回复 回复 引用 0
      • Z
        zhanglu 最后由 编辑

        database {
        profile = "slick.jdbc.PostgresProfile$"
        db {
        driver = "org.postgresql.Driver"
        url = "jdbc:postgresql://172.17.0.1:5437/cromwell"
        user = "postgres"
        password = "genostack123456"
        port = 5437
        connectionTimeout = 5000
        }
        }
        akka.http.server.request-timeout = 100s
        docker {
        hash-lookup {
        method = "local"
        }
        }

        backend {
        default = slurm

        providers {
        slurm {
        actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
        config {
        runtime-attributes = """
        Int cpu = 2
        String? docker
        """
        root = "/cephfs_data/slurm_hpc2/genostack_v3/genostack_cromwell/cromwell-executions"
        dockerRoot = "/cephfs_data/slurm_hpc2/genostack_v3/genostack_cromwell/cromwell-executions"
        submit-docker = """
        # Pull the image using the head node, in case our workers don't have network access
        docker pull ${docker}

              sbatch \
        -J ${job_name} \
        -D ${cwd} \
        ${"-c " + cpu} \
       --wrap "docker run -v /cephfs_data/slurm_hpc2:/cephfs_data/slurm_hpc2 ${docker} ${job_shell} ${docker_script}"
    """
    kill = "scancel ${job_id}"
    check-alive = "squeue -j ${job_id}"
    job-id-regex = "Submitted batch job (\\d+).*"
  }
}

        }

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        • Z
          zhanglu 最后由 编辑

          workflow hello {
          String aaa = "aaaaaaaaaaaaaa"
          call path_to_pair {
          input:
          aaa = aaa
          }
          }
          task path_to_pair {
          String aaa
          command {
          sleep 20s
          echo '${aaa}' > out.txt
          }
          runtime {
          cpu: 1
          docker: "dockerhub.genostack.com:8090/library/fileparse:v1"
          }
          output {
          File out = "out.txt"
          }
          }

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          • Z
            zhanglu 最后由 编辑

            hello1.wdl

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            • Z
              zhanglu 最后由 编辑 

                  submit = """
        sbatch \
          --wait \
          -J ${job_name} \
          -D ${cwd} \
          -t ${runtime_minutes} \
          ${"-c " + cpus} \
          --mem-per-cpu=${requested_memory_mb_per_core} \
          --wrap "/bin/bash ${docker_script}"
    """
              1 条回复 最后回复 回复 引用 0
              • Z
                zhanglu 最后由 编辑 

                    submit = """
        sbatch -J ${job_name} -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} -p ${queue} \
        ${"-n " + cpus} \
        --mem-per-cpu=${requested_memory_mb_per_core} \
        --wrap "/usr/bin/env bash ${script}"
    """
                1 条回复 最后回复 回复 引用 0
                • Z
                  zhanglu 最后由 编辑

                  mpirun -np 20 /opt/software/lammps-7Feb2024/src/lmp_oneapi -sf gpu -pk gpu 1 neigh no -in in.rigid

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                  • Z
                    zhanglu 最后由 编辑

                    nerdctl pull dyrnq/pause:3.9
                    nerdctl pull dyrnq/coredns:v1.10.1
                    nerdctl pull dyrnq/k8s-dns-node-cache:1.22.20
                    nerdctl pull dyrnq/metrics-server:v0.6.4
                    nerdctl pull dyrnq/local-volume-provisioner:v2.5.0
                    nerdctl pull dyrnq/controller:v1.8.1
                    nerdctl pull dyrnq/csi-attacher:v3.3.0
                    nerdctl pull dyrnq/csi-provisioner:v3.0.0
                    nerdctl pull dyrnq/csi-snapshotter:v5.0.0
                    nerdctl pull dyrnq/csi-resizer:v1.3.0
                    nerdctl pull dyrnq/csi-node-driver-registrar:v2.4.0
                    nerdctl pull dyrnq/livenessprobe:v2.5.0
                    nerdctl pull dockergroo/cluster-proportional-autoscaler:v1.8.8

                    nerdctl tag dyrnq/pause:3.9 registry.k8s.io/pause:3.9
                    nerdctl tag dyrnq/pause:3.9 registry.k8s.io/kube-proxy/pause:3.9
                    nerdctl tag dyrnq/coredns:v1.10.1 registry.k8s.io/coredns/coredns:v1.10.1
                    nerdctl tag dyrnq/k8s-dns-node-cache:1.22.20 registry.k8s.io/dns/k8s-dns-node-cache:1.22.20
                    nerdctl tag dyrnq/metrics-server:v0.6.4 registry.k8s.io/metrics-server/metrics-server:v0.6.4
                    nerdctl tag dyrnq/local-volume-provisioner:v2.5.0 registry.k8s.io/sig-storage/local-volume-provisioner:v2.5.0
                    nerdctl tag dyrnq/controller:v1.8.1 registry.k8s.io/ingress-nginx/controller:v1.8.1
                    nerdctl tag dyrnq/csi-attacher:v3.3.0 registry.k8s.io/sig-storage/csi-attacher:v3.3.0
                    nerdctl tag dyrnq/csi-provisioner:v3.0.0 registry.k8s.io/sig-storage/csi-provisioner:v3.0.0
                    nerdctl tag dyrnq/csi-snapshotter:v5.0.0 registry.k8s.io/sig-storage/csi-snapshotter:v5.0.0
                    nerdctl tag dyrnq/csi-resizer:v1.3.0 registry.k8s.io/sig-storage/csi-resizer:v1.3.0
                    nerdctl tag dyrnq/csi-node-driver-registrar:v2.4.0 registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.4.0
                    nerdctl tag dyrnq/livenessprobe:v2.5.0 registry.k8s.io/sig-storage/livenessprobe:v2.5.0
                    nerdctl tag dockergroo/cluster-proportional-autoscaler:v1.8.8 registry.k8s.io/cpa/cluster-proportional-autoscaler:v1.8.8
                    nerdctl pull dyrnq/kube-apiserver:v1.27.7
                    nerdctl tag dyrnq/kube-apiserver:v1.27.7 registry.k8s.io/kube-apiserver:v1.27.7
                    nerdctl pull dyrnq/kube-controller-manager:v1.27.7
                    nerdctl tag dyrnq/kube-controller-manager:v1.27.7 registry.k8s.io/kube-controller-manager:v1.27.7
                    nerdctl pull dyrnq/kube-scheduler:v1.27.7
                    nerdctl tag dyrnq/kube-scheduler:v1.27.7 registry.k8s.io/kube-scheduler:v1.27.7
                    nerdctl pull dyrnq/kube-proxy:v1.27.7
                    nerdctl tag dyrnq/kube-proxy:v1.27.7 registry.k8s.io/kube-proxy:v1.27.7

                    初于钟情:
                    qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads bold_derep1_seqs.qza --i-reference-taxonomy bold_derep1_taxa.qza --o-classifier bold_derep1_classifier.qza

                    初于钟情:
                    qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads bold_anml_seqs.qza --i-reference-taxonomy bold_anml_taxa.qza --o-classifier bold_anml_classifer_anneng.qza &

                    nerdctl pull docker/desktop-kubernetes-pause:3.5
                    nerdctl tag docker/desktop-kubernetes-pause:3.5 k8s.gcr.io/pause:3.5

                    nerdctl pull cnplat/kube-scheduler:v1.19.13
                    nerdctl tag cnplat/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                    nerdctl pull kubeon/pause:3.5
                    nerdctl tag kubeon/pause:3.5 k8s.gcr.io/pause:3.5

                    nerdctl pull dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13
                    nerdctl tag dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                    nerdctl pull jupyterhub/configurable-http-proxy:4.5.0
                    nerdctl tag jupyterhub/configurable-http-proxy:4.5.0 jupyterhub/configurable-http-proxy:4.5.0

                    nerdctl rmi k8s.gcr.io/kube-scheduler:v1.19.13 --force
                    nerdctl rmi k8s.gcr.io/pause:3.5 --force

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                    • Z
                      zhanglu 最后由 编辑

                      nerdctl pull docker/desktop-kubernetes-pause:3.5
                      nerdctl tag docker/desktop-kubernetes-pause:3.5 k8s.gcr.io/pause:3.5

                      nerdctl pull cnplat/kube-scheduler:v1.19.13
                      nerdctl tag cnplat/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                      nerdctl pull kubeon/pause:3.5
                      nerdctl tag kubeon/pause:3.5 k8s.gcr.io/pause:3.5

                      nerdctl pull dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13
                      nerdctl tag dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                      nerdctl pull jupyterhub/configurable-http-proxy:4.5.0
                      nerdctl tag jupyterhub/configurable-http-proxy:4.5.0 jupyterhub/configurable-http-proxy:4.5.0

                      nerdctl rmi k8s.gcr.io/kube-scheduler:v1.19.13 --force
                      nerdctl rmi k8s.gcr.io/pause:3.5 --force

                      1 条回复 最后回复 回复 引用 0
                      • Z
                        zhanglu 最后由 编辑

                        nerdctl pull dyrnq/csi-node-driver-registrar:v2.9.1
                        nerdctl pull dyrnq/csi-resizer:v1.9.2
                        nerdctl pull dyrnq/csi-provisioner:v3.6.2
                        nerdctl pull dyrnq/csi-snapshotter:v6.3.2
                        nerdctl pull dyrnq/csi-attacher:v4.4.2
                        nerdctl tag dyrnq/csi-node-driver-registrar:v2.9.1 registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.9.1
                        nerdctl tag dyrnq/csi-resizer:v1.9.2 registry.k8s.io/sig-storage/csi-resizer:v1.9.2
                        nerdctl tag dyrnq/csi-provisioner:v3.6.2 registry.k8s.io/sig-storage/csi-provisioner:v3.6.2
                        nerdctl tag dyrnq/csi-snapshotter:v6.3.2 registry.k8s.io/sig-storage/csi-snapshotter:v6.3.2
                        nerdctl tag dyrnq/csi-attacher:v4.4.2 registry.k8s.io/sig-storage/csi-attacher:v4.4.2

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                        • Z
                          zhanglu 最后由 编辑

                          {
                          "url":"/home/genostack/workspace/test/sample.vcf",
                          "data_detection": ["561","297","363","556","446","417","382","338","431","18","286","295","356","375","406","326","562","35","61","359","26","163","69","336","45","370","91","63","426","94","103","50","70","20","174","30","251","47","109","148","23","74","555","557","12","418","87","310","355","19","17","83","281","283","419","304","395","404","369","8","298","54","374","300","483","518","464","474","333","187","496","66","68","67","560","11","416","16","420","503","78","143","402","272","81","421","40","422","226","65","55","9","77","153","202","60","339","444","53","386","379","277","414","85","367","387","371","312","64","408","390","334","276","179","33","354","472","274","228","351","384","152","486","505","199","481","240","182","450","337","280","327","289","209","176","263","291","380","377","500","275","75","432","399","378","436","443","456","278","314","335","292","190","391","341","460","449","452","302","321","485","198","440","476","495","383","330","361","407","150","466","126","13","101","211","185","477","479","497","396","388","307","348","389","293","32","400","37","360","403","34","296","364","427","368","411","318","340","349","430","362","309","475","439","373","457","366","96","365","458","465","106","80","57","93","320","517","52","41","124","86","31","73","316","39","98","471","22","322","342","270","453","398","352","350","357","433","405","4","42","62","305","376","249","104","242","10","223","217","268","559","7","97","2","285","325","558","287","313","288","3","331","345","5","27","438","282","353","441","343","372","308","205","139","506","191","225","315","284","442","501","435","434","306","164","259","100","347","188","468","467","328","158","180","173","424","303","447","410","344","448","413","401","512","319","423","513","428","459","445","461","279","301","72","224","429","454","262","317","392","412","290","294","409","511","397","323","425","140","385","437","451","273","487","469","136","488","499","137","346","490","254"],
                          "data_module": []
                          }

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                          • Z
                            zhanglu 最后由 编辑

                            http://192.168.0.143:8086/gene/file/read

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                            • Z
                              zhanglu 最后由 编辑

                              id 272
                              name 3-羟-3-甲基戊二酰辅酶A裂解酶缺乏症
                              rsid rs763494292
                              geneType AC
                              spare A
                              genetypes AC,CC,AA
                              Gene HMGCL
                              result 携带

                              1 条回复 最后回复 回复 引用 0
                              • Z
                                zhanglu 最后由 编辑

                                B型家族性高胆固醇血症

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                                • Z
                                  zhanglu 最后由 编辑

                                  马德隆畸形
                                  geneType CG
                                  spare G,T
                                  gene SHOX
                                  genetypes CG,CT,CC,GG,TT
                                  result 携带

                                  1 条回复 最后回复 回复 引用 0
                                  • Z
                                    zhanglu 最后由 编辑

                                    酪氨酸血症II型
                                    geneType AG
                                    spare A
                                    gene TAT
                                    genetypes AG,GG,AA
                                    result 携带

                                    1 条回复 最后回复 回复 引用 0
                                    • Z
                                      zhanglu 最后由 编辑

                                      SELECT
                                      rs.rsid AS rsId,
                                      rg.pair AS genotype,
                                      rd.spare AS spare,
                                      rd.score AS genotypeScore,
                                      rd.pk AS pk,
                                      rd.efficacy AS efficacy,
                                      rd.toxicity AS toxicity,
                                      rd.dosage AS dosage,
                                      rd.freq AS freq,
                                      rd.detection_id AS detectionId,
                                      rd.description,
                                      report_genes.name as gene
                                      FROM
                                      report_detection_genotype as rd
                                      LEFT JOIN report_genotypes as rg ON rg.ID = rd.genotype_id
                                      LEFT JOIN report_snp as rs ON rs.ID = rg.snp_id
                                      LEFT JOIN report_genes on report_genes.id = rs.genes_id
                                      WHERE
                                      rd.detection_id IN

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                                      • Z
                                        zhanglu 最后由 编辑

                                        a.txt

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                                        • Z
                                          zhanglu 最后由 编辑

                                          kubectl get jobs -o json | jq -r '.items[] | select((.status.succeeded//0) > 0) | .metadata.name' | xargs kubectl delete job

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                                          • Z
                                            zhanglu 最后由 编辑

                                            docker run
                                            -v /cephfs_data/GreatHealth/postgres:/var/lib/postgresql/data
                                            -e POSTGRES_PASSWORD=genostack123456 -p 5433:5432 -d dockerhub.genostack.com:8090/library/postgres:10

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