暗能星系
    • 登录
    • 搜索

    tmp

    张渌
    2
    262
    1755
    正在加载更多帖子
    • 从旧到新
    • 从新到旧
    • 最多赞同
    回复
    • 在新帖中回复
    登录后回复
    此主题已被删除。只有拥有主题管理权限的用户可以查看。
    • Z
      zhanglu 最后由 编辑

      slurm.sql

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

        #!/bin/bash
        #SBATCH -J test
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --comment=test
        date
        hostname
        touch /cephfs_data/aaaaaaaaaaaa.txt
        sleep 10s
        date

        1 条回复 最后回复 回复 引用 0
        • 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+).*"
  }
}

            }

            1 条回复 最后回复 回复 引用 0
            • 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"
              }
              }

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

                hello1.wdl

                1 条回复 最后回复 回复 引用 0
                • 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

                      1 条回复 最后回复 回复 引用 0
                      • 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

                        1 条回复 最后回复 回复 引用 0
                        • 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

                            1 条回复 最后回复 回复 引用 0
                            • 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": []
                              }

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

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

                                1 条回复 最后回复 回复 引用 0
                                • 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

                                    1 条回复 最后回复 回复 引用 0
                                    • 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

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

                                            a.txt

                                            1 条回复 最后回复 回复 引用 0
                                            • First post
                                              Last post
                                            Powered by 暗能星系