暗能星系

zhanglu

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+).*"
  }
}

}

zhanglu

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"
}
}

zhanglu

hello1.wdl

zhanglu

    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}"
    """

zhanglu

    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}"
    """

zhanglu

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

zhanglu

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

zhanglu

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

zhanglu

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

zhanglu

{
"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": []
}

zhanglu

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

zhanglu

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

zhanglu

B型家族性高胆固醇血症

zhanglu

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

zhanglu

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

zhanglu

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

zhanglu

a.txt

zhanglu

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

zhanglu

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

zhanglu

docker重启失败,重装docker和恢复服务操作：

yum remove docker*
yum install docker-ce
配置/etc/docker/daimon.json
systemctl start docker
systemctl enable docker
拉取镜像
docker pull dockerhub.genostack.com:8090/library/ceph:v1.10.8
docker tag dockerhub.genostack.com:8090/library/ceph:v1.10.8 rook/ceph:v1.10.8
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/kubernetesui_metrics-scraper:v1.0.6
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/library_nginx:1.19
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/coredns:1.7.0
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/dns_k8s-dns-node-cache:1.16.0
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/ingress-nginx_controller:v0.41.2
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/kube-apiserver:v1.19.7
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/kube-controller-manager:v1.19.7
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/kube-proxy:v1.19.7
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/kube-scheduler:v1.19.7
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/pause:3.2
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/pause:3.3
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/kubernetesui_dashboard-amd64:v2.1.0
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/cpa_cluster-proportional-autoscaler-amd64:1.8.3
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/calico_cni:v3.16.5
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/calico_kube-controllers:v3.16.5
docker pull dockerhub.genostack.com:8090/k8s/kubernetes-kubespray/calico_node:v3.16.5

docker pull dockerhub.genostack.com:8090/rook/cephcsi/cephcsi:v3.7.2
docker pull dockerhub.genostack.com:8090/rook/csi-node-driver-registrar:v2.5.1
docker pull dockerhub.genostack.com:8090/rook/csi-resizer:v1.6.0
docker pull dockerhub.genostack.com:8090/rook/csi-provisioner:v3.3.0
docker pull dockerhub.genostack.com:8090/rook/csi-snapshotter:v6.1.0
docker pull dockerhub.genostack.com:8090/rook/csi-attacher:v4.0.0
docker pull dockerhub.genostack.com:8090/rook/ceph/ceph:v17.2.5

docker tag dockerhub.genostack.com:8090/rook/cephcsi/cephcsi:v3.7.2 quay.io/cephcsi/cephcsi:v3.7.2
docker tag dockerhub.genostack.com:8090/rook/csi-node-driver-registrar:v2.5.1 registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1
docker tag dockerhub.genostack.com:8090/rook/csi-resizer:v1.6.0 registry.k8s.io/sig-storage/csi-resizer:v1.6.0
docker tag dockerhub.genostack.com:8090/rook/csi-provisioner:v3.3.0 registry.k8s.io/sig-storage/csi-provisioner:v3.3.0
docker tag dockerhub.genostack.com:8090/rook/csi-snapshotter:v6.1.0 registry.k8s.io/sig-storage/csi-snapshotter:v6.1.0
docker tag dockerhub.genostack.com:8090/rook/csi-attacher:v4.0.0 registry.k8s.io/sig-storage/csi-attacher:v4.0.0
docker tag dockerhub.genostack.com:8090/rook/ceph/ceph:v17.2.5 quay.io/ceph/ceph:v17.2.5

启动服务：
（1）检查swap内存，需要处于关闭状态，关闭命令：
swapoff -a
(2) 重启kubelet:
systemctl restart kubelet
(3) 等待集群重启，正常情况下执行docker ps,会有很多容器启动，
查看服务： kubectl get pod -n kube-system
存储服务： kubectl get pod -n rook-ceph

tmp