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liezl200/cloudgene install Secret

Created January 3, 2020 01:21
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cloudgene install
Last login: Mon Dec 23 16:36:05 on ttys006
gcloud compute instances list
(base) liezls-mbp:~ lie$ gcloud compute instances list
NAME ZONE MACHINE_TYPE PREEMPTIBLE INTERNAL_IP EXTERNAL_IP STATUS
gke-hello-cluster-default-pool-b7fd8074-c33c us-central1-a n1-standard-1 10.128.0.2 34.69.225.127 RUNNING
gke-hello-cluster-default-pool-b7fd8074-p4t1 us-central1-a n1-standard-1 10.128.0.3 35.188.197.250 RUNNING
Updates are available for some Cloud SDK components. To install them,
please run:
$ gcloud components update
To take a quick anonymous survey, run:
$ gcloud alpha survey
(base) liezls-mbp:~ lie$
(base) liezls-mbp:~ lie$ ${PROJECT_ID}
(base) liezls-mbp:~ lie$ ${PROJECT_ID}expo
(base) liezls-mbp:~ lie$ export PROJECT_ID = orchid-434cb
-bash: export: `=': not a valid identifier
-bash: export: `orchid-434cb': not a valid identifier
(base) liezls-mbp:~ lie$ export PROJECT_ID=orchid-434cb
(base) liezls-mbp:~ lie$ ${PROJECT_ID}
-bash: orchid-434cb: command not found
(base) liezls-mbp:~ lie$ kubectl create deployment hello-web --image=gcr.io/${PROJECT_ID}/hello-app:v1
deployment.apps/hello-web created
(base) liezls-mbp:~ lie$ kubectl get pods
NAME READY STATUS RESTARTS AGE
hello-web-68b55d7b97-hqjkr 0/1 ContainerCreating 0 2s
(base) liezls-mbp:~ lie$
(base) liezls-mbp:~ lie$ kubectl expose deployment hello-web --type=LoadBalancer --port 80 --target-port 8080
service/hello-web exposed
(base) liezls-mbp:~ lie$ kubectl get service
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
hello-web LoadBalancer 10.15.251.132 <pending> 80:31509/TCP 24s
kubernetes ClusterIP 10.15.240.1 <none> 443/TCP 9d
(base) liezls-mbp:~ lie$
(base) liezls-mbp:~ lie$ kubectl get service
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
hello-web LoadBalancer 10.15.251.132 35.226.184.197 80:31509/TCP 72s
kubernetes ClusterIP 10.15.240.1 <none> 443/TCP 9d
(base) liezls-mbp:~ lie$ kubectl delete service hello-web
service "hello-web" deleted
(base) liezls-mbp:~ lie$
(base) liezls-mbp:~ lie$ gcloud container clusters delete hello-cluster
The following clusters will be deleted.
- [hello-cluster] in [us-central1-a]
Do you want to continue (Y/n)?
Deleting cluster hello-cluster...⠏
Deleting cluster hello-cluster...done.
Deleted [https://container.googleapis.com/v1/projects/orchid-434cb/zones/us-central1-a/clusters/hello-cluster].
(base) liezls-mbp:~ lie$ Y
-bash: Y: command not found
(base) liezls-mbp:~ lie$ ls
23_19-Type2Diabetes_March2019.pdf
23andme-uploader
23andme_static
2vcf-0.4.0
2vcf_0.4.0_Darwin_i386
Applications
Desktop
Documents
Downloads
Library
Liezl Puzon BRCA1_BRCA2 (Selected Variants) Report - 23andMe.pdf
Liezl Puzon Type 2 Diabetes Report - 23andMe.pdf
Movies
Music
Pictures
Public
Tools
app_backup.js
bcftools-1.10
checkVCF-20140116
firebase-app-starter
genome_snp_map
google-cloud-sdk
google-cloud-sdk-272.0.0-darwin-x86_64.tar.gz
htslib-1.10.2
iCARE
kubernetes-engine-samples
login_backup.html
my_NC_012920_1_variants.json
my_marker_NC_000001_10_chromosome_1.json
my_variant_NC_000001_10_chromosome_1.json
my_variant_NC_000012_11_chromosome_12.json
my_variant_NC_000013_10_chromosome_13.json
my_variant_NC_000014_8_chromosome_14.json
my_variant_NC_000015_9_chromosome_15.json
node_modules
opt
orchid-firebase-app
orchid-web-server
orchid-web-server2
orchidhealth.com
package-lock.json
plink2
plink2.log
plink_mac_20191130
prs-tools
recover
samtools-1.10
tabix-0.2.6
upload_file_backup.js
variant_NC_000015_9_chromosome_15.json
vcftools-vcftools-954e607
(base) liezls-mbp:~ lie$ mkdir imputationserver-data
(base) liezls-mbp:~ lie$ docker run -d -p 8080:80 -v /home/lie/imputationserver-data/:/data/ genepi/imputationserver:v1.2.4
b895f8eb2571ea5a814249ee0cd66c1ea7b24dce050bab4f06be77a8e4f4565d
docker: Error response from daemon: Mounts denied:
The path /home/lie/imputationserver-data/
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info.
.
(base) liezls-mbp:~ lie$ ls /home/lie/imputationserver-data/
ls: /home/lie/imputationserver-data/: No such file or directory
(base) liezls-mbp:~ lie$ mkdir /home/lie/imputationserver-data/
mkdir: /home/lie: No such file or directory
(base) liezls-mbp:~ lie$ ls
23_19-Type2Diabetes_March2019.pdf
23andme-uploader
23andme_static
2vcf-0.4.0
2vcf_0.4.0_Darwin_i386
Applications
Desktop
Documents
Downloads
Library
Liezl Puzon BRCA1_BRCA2 (Selected Variants) Report - 23andMe.pdf
Liezl Puzon Type 2 Diabetes Report - 23andMe.pdf
Movies
Music
Pictures
Public
Tools
app_backup.js
bcftools-1.10
checkVCF-20140116
firebase-app-starter
genome_snp_map
google-cloud-sdk
google-cloud-sdk-272.0.0-darwin-x86_64.tar.gz
htslib-1.10.2
iCARE
imputationserver-data
kubernetes-engine-samples
login_backup.html
my_NC_012920_1_variants.json
my_marker_NC_000001_10_chromosome_1.json
my_variant_NC_000001_10_chromosome_1.json
my_variant_NC_000012_11_chromosome_12.json
my_variant_NC_000013_10_chromosome_13.json
my_variant_NC_000014_8_chromosome_14.json
my_variant_NC_000015_9_chromosome_15.json
node_modules
opt
orchid-firebase-app
orchid-web-server
orchid-web-server2
orchidhealth.com
package-lock.json
plink2
plink2.log
plink_mac_20191130
prs-tools
recover
samtools-1.10
tabix-0.2.6
upload_file_backup.js
variant_NC_000015_9_chromosome_15.json
vcftools-vcftools-954e607
(base) liezls-mbp:~ lie$ ls /
Applications etc
Library home
Network installer.failurerequests
System net
Users private
Volumes sbin
bin tmp
cores usr
dev var
(base) liezls-mbp:~ lie$ ls /home
(base) liezls-mbp:~ lie$ ls /home/lie
ls: /home/lie: No such file or directory
(base) liezls-mbp:~ lie$ ls /home/
(base) liezls-mbp:~ lie$ ls ~
23_19-Type2Diabetes_March2019.pdf
23andme-uploader
23andme_static
2vcf-0.4.0
2vcf_0.4.0_Darwin_i386
Applications
Desktop
Documents
Downloads
Library
Liezl Puzon BRCA1_BRCA2 (Selected Variants) Report - 23andMe.pdf
Liezl Puzon Type 2 Diabetes Report - 23andMe.pdf
Movies
Music
Pictures
Public
Tools
app_backup.js
bcftools-1.10
checkVCF-20140116
firebase-app-starter
genome_snp_map
google-cloud-sdk
google-cloud-sdk-272.0.0-darwin-x86_64.tar.gz
htslib-1.10.2
iCARE
imputationserver-data
kubernetes-engine-samples
login_backup.html
my_NC_012920_1_variants.json
my_marker_NC_000001_10_chromosome_1.json
my_variant_NC_000001_10_chromosome_1.json
my_variant_NC_000012_11_chromosome_12.json
my_variant_NC_000013_10_chromosome_13.json
my_variant_NC_000014_8_chromosome_14.json
my_variant_NC_000015_9_chromosome_15.json
node_modules
opt
orchid-firebase-app
orchid-web-server
orchid-web-server2
orchidhealth.com
package-lock.json
plink2
plink2.log
plink_mac_20191130
prs-tools
recover
samtools-1.10
tabix-0.2.6
upload_file_backup.js
variant_NC_000015_9_chromosome_15.json
vcftools-vcftools-954e607
(base) liezls-mbp:~ lie$ pwd
/Users/lie
(base) liezls-mbp:~ lie$ docker run -d -p 8080:80 -v /Users/lie/imputationserver-data/:/data/ genepi/imputationserver:v1.2.4
d8ef75fbf671b821034a17573efb3f4067bb16fd22f29b9500d37408a30f0816
(base) liezls-mbp:~ lie$ curl http://localhost:8080
curl: (52) Empty reply from server
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
d8ef75fbf671 genepi/imputationserver:v1.2.4 "/usr/bin/startup" About a minute ago Up About a minute 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8080->80/tcp stoic_allen
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
d8ef75fbf671 genepi/imputationserver:v1.2.4 "/usr/bin/startup" About a minute ago Up About a minute 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8080->80/tcp stoic_allen
(base) liezls-mbp:~ lie$ docker container lsdocker run -d -p 8080:80 genepi/cloudgene
unknown shorthand flag: 'd' in -d
See 'docker container --help'.
Usage: docker container COMMAND
Manage containers
Commands:
attach Attach local standard input, output, and error streams to a running container
commit Create a new image from a container's changes
cp Copy files/folders between a container and the local filesystem
create Create a new container
diff Inspect changes to files or directories on a container's filesystem
exec Run a command in a running container
export Export a container's filesystem as a tar archive
inspect Display detailed information on one or more containers
kill Kill one or more running containers
logs Fetch the logs of a container
ls List containers
pause Pause all processes within one or more containers
port List port mappings or a specific mapping for the container
prune Remove all stopped containers
rename Rename a container
restart Restart one or more containers
rm Remove one or more containers
run Run a command in a new container
start Start one or more stopped containers
stats Display a live stream of container(s) resource usage statistics
stop Stop one or more running containers
top Display the running processes of a container
unpause Unpause all processes within one or more containers
update Update configuration of one or more containers
wait Block until one or more containers stop, then print their exit codes
Run 'docker container COMMAND --help' for more information on a command.
(base) liezls-mbp:~ lie$
(base) liezls-mbp:~ lie$ docker run -d -p 8080:80 genepi/cloudgene
Unable to find image 'genepi/cloudgene:latest' locally
^C
(base) liezls-mbp:~ lie$ docker run -d -p 8081:81 genepi/cloudgene
Unable to find image 'genepi/cloudgene:latest' locally
latest: Pulling from genepi/cloudgene
a7344f52cb74: Pulling fs layer
515c9bb51536: Pulling fs layer
e1eabe0537eb: Pulling fs layer
4701f1215c13: Waiting
dfa8f64d8158: Waiting
658a06cdd04f: Waiting
9c41c7761fc7: Waiting
585c675aa7b7: Waiting
58b8a9f3817a: Waiting
4383aa756fdd: Waiting
9ada9a155f8e: Waiting
3f6efa9a1568: Waiting
61fdb5ccb2b2: Waiting
b9e2a86ef41a: Pulling fs layer
3fc3936f2c35: Pulling fs layer
851c4bce6d2e: Pulling fs layer
04cb27b862cb: Pulling fs layer
87c6f72817f9: Pulling fs layer
487ededf080e: Pulling fs layer
45a27374931f: Pulling fs layer
d997c2c42a1e: Pull complete
a4b6e5cd05e5: Pull complete
02b98918dabb: Pull complete
8a2e7ee11257: Pull complete
b480800e1837: Pull complete
bc137d2ef322: Pull complete
3e12605d2df7: Pull complete
31a43d6bfab8: Pull complete
0ff2e89a9ead: Pull complete
19c677f6b97d: Pull complete
6729fb0542e1: Pull complete
0758834c2b6a: Pull complete
bae4d5f8dd48: Pull complete
1245a391c4a2: Pull complete
ebae92d3c4e6: Pull complete
f26b47d259c8: Pull complete
579e385023c9: Pull complete
6f45948c5f8b: Pull complete
ddc5bf66cdad: Pull complete
5bbc35a9dee2: Pull complete
9b6b0227ce19: Pull complete
ab3aac7ea5ce: Pull complete
6f5896c6e08b: Pull complete
8dea39d29cd0: Pull complete
Digest: sha256:6a8a6ec984bb8cc91889673fd5d0ca9095a0fa2e89790d7706d0cb7ed6fb9b0a
Status: Downloaded newer image for genepi/cloudgene:latest
adefde2f84c3d3f3541a057cd46dcc35dbd98bc2eef5c306e96bbd0b6dcc4f62
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
adefde2f84c3 genepi/cloudgene "/usr/bin/startup" 44 seconds ago Up 42 seconds 80/tcp, 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8081->81/tcp zealous_mccarthy
d8ef75fbf671 genepi/imputationserver:v1.2.4 "/usr/bin/startup" 13 minutes ago Up 13 minutes 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8080->80/tcp stoic_allen
(base) liezls-mbp:~ lie$ docker container ls
^C
(base) liezls-mbp:~ lie$
(base) liezls-mbp:~ lie$ docker container ls
^C
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
adefde2f84c3 genepi/cloudgene "/usr/bin/startup" 4 minutes ago Up 4 minutes 80/tcp, 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8081->81/tcp zealous_mccarthy
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
adefde2f84c3 genepi/cloudgene "/usr/bin/startup" 4 minutes ago Up 4 minutes 80/tcp, 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8081->81/tcp zealous_mccarthy
(base) liezls-mbp:~ lie$ docker run -d -p 8080:80 genepi/cloudgene
c77e7abc47af1252da794cc35500230ca541f0d87f523e80bfc94c272acfc682
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
c77e7abc47af genepi/cloudgene "/usr/bin/startup" 8 seconds ago Up 6 seconds 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8080->80/tcp cranky_shirley
adefde2f84c3 genepi/cloudgene "/usr/bin/startup" 5 minutes ago Up 5 minutes 80/tcp, 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8081->81/tcp zealous_mccarthy
(base) liezls-mbp:~ lie$ docker container ls
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
c77e7abc47af genepi/cloudgene "/usr/bin/startup" About a minute ago Up About a minute 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8080->80/tcp cranky_shirley
adefde2f84c3 genepi/cloudgene "/usr/bin/startup" 6 minutes ago Up 6 minutes 80/tcp, 50010/tcp, 50020/tcp, 50030/tcp, 50050/tcp, 50070/tcp, 50075/tcp, 50090/tcp, 0.0.0.0:8081->81/tcp zealous_mccarthy
(base) liezls-mbp:~ lie$ docker run -d -p 8080:80 -v /Users/lie/imputationserver-data/:/data/ genepi/imputationserver:v1.2.4
e4c370a8eacf474199db9ce370044a3eae4310f853377dbd888d10ffcc867633
docker: Error response from daemon: driver failed programming external connectivity on endpoint thirsty_spence (2dc5b28dd1293bb279385f771a7b802c393a39f8311b68ecd4186ded936b1e2c): Bind for 0.0.0.0:8080 failed: port is already allocated.
(base) liezls-mbp:~ lie$ docker kill c77e7abc47af
c77e7abc47af
(base) liezls-mbp:~ lie$ docker kill adefde2f84c3
adefde2f84c3
(base) liezls-mbp:~ lie$ docker run -d -p 8080:80 -v /Users/lie/imputationserver-data/:/data/ genepi/imputationserver:v1.2.4
093ca3dac98709ce56e16fc357d1f8190a38338792ee101a31fed4181aa6eacb
(base) liezls-mbp:~ lie$ cloudgene
-bash: cloudgene: command not found
(base) liezls-mbp:~ lie$ pwd
/Users/lie
(base) liezls-mbp:~ lie$ mkdir cloudgen
(base) liezls-mbp:~ lie$ rmdir cloudgen
(base) liezls-mbp:~ lie$ mkdir cloudgene
(base) liezls-mbp:~ lie$ cd cloudgene
(base) liezls-mbp:cloudgene lie$ curl -s install.cloudgene.io | bash
Installing Cloudgene 2.0.5...
Downloading Cloudgene https://github.com/genepi/cloudgene/releases/download/v2.0.5/cloudgene-installer.sh...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 613 0 613 0 0 2023 0 --:--:-- --:--:-- --:--:-- 2023
100 30.3M 100 30.3M 0 0 6138k 0 0:00:05 0:00:05 --:--:-- 7337k
Verifying archive integrity... 100% All good.
Uncompressing Install
script=Cloudgene
scriptargs=2.0.5 makeself.sh 100%
Cloudgene 2.0.5 installation completed. Have fun!
(base) liezls-mbp:cloudgene lie$ ./cloudgene version
Cloudgene 2.0.5
http://www.cloudgene.io
(c) 2009-2019 Lukas Forer and Sebastian Schoenherr
Built by travis on 2019-12-12T16:43:01Z
Built by travis on 2019-12-12T16:43:01Z
(base) liezls-mbp:cloudgene lie$
(base) liezls-mbp:cloudgene lie$ cloudgene
-bash: cloudgene: command not found
(base) liezls-mbp:cloudgene lie$ ./cloudgene
Cloudgene 2.0.5
http://www.cloudgene.io
(c) 2009-2019 Lukas Forer and Sebastian Schoenherr
Built by travis on 2019-12-12T16:43:01Z
Built by travis on 2019-12-12T16:43:01Z
usage: cloudgene <tool> <params>
Available Tools:
gh
server
install
github-install
verify-cluster
plugins
ls
clone
run
version
remove
validate
(base) liezls-mbp:cloudgene lie$ ./cloudgene install
Cloudgene 2.0.5
http://www.cloudgene.io
(c) 2009-2019 Lukas Forer and Sebastian Schoenherr
Built by travis on 2019-12-12T16:43:01Z
Built by travis on 2019-12-12T16:43:01Z
Usage: cloudgeneinstall <filename|url|github>
(base) liezls-mbp:cloudgene lie$ ./cloudgene install https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip
Cloudgene 2.0.5
http://www.cloudgene.io
(c) 2009-2019 Lukas Forer and Sebastian Schoenherr
Built by travis on 2019-12-12T16:43:01Z
Built by travis on 2019-12-12T16:43:01Z
Installing application https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip...
^[[A^[[A^[[B^[[B^C(base) liezls-mcloudgene
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