Linux使用Docker总结

红鲤绿与鱼

已于 2024-08-01 13:32:01 修改

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文章标签： linux docker

于 2024-08-01 13:29:13 首次发布

本文链接：https://blog.csdn.net/m0_60116853/article/details/140779220

版权

首先，先了解Docker到底是什么？
参考：

先补充一下有权限读`root`时的命令

善用cd /

[ATCG03@AIBIO03 ~]$ cd /
[ATCG03@AIBIO03 /]$ ll
total 68
lrwxrwxrwx.   1 root root     7 Jul 18  2023 bin -> usr/bin
dr-xr-xr-x.   5 root root  4096 Jul 18  2023 boot
drwxr-xr-x   19 root root  2980 Jul 29 21:50 dev
drwxr-xr-x.  96 root root 12288 Jul 29 21:49 etc
drwxr-xr-x.  32 root root  4096 Jul 28 09:46 home
lrwxrwxrwx.   1 root root     7 Jul 18  2023 lib -> usr/lib
lrwxrwxrwx.   1 root root     9 Jul 18  2023 lib64 -> usr/lib64
drwx------.   2 root root 16384 Jul 18  2023 lost+found
drwxr-xr-x.   2 root root  4096 Apr 11  2018 media
drwxr-xr-x.   2 root root  4096 Apr 11  2018 mnt
drwxr-xr-x.   3 root root  4096 Sep 19  2023 opt
dr-xr-xr-x  313 root root     0 Jul 29 21:48 proc
dr-xr-x---.  23 root root  4096 Aug  1 09:18 root
drwxr-xr-x   30 root root   980 Jul 29 21:49 run
lrwxrwxrwx.   1 root root     8 Jul 18  2023 sbin -> usr/sbin
drwxr-xr-x.   2 root root  4096 Apr 11  2018 srv
dr-xr-xr-x   13 root root     0 Jul 30 10:03 sys
drwxrwxrwt.  39 root root  4096 Aug  1 09:38 tmp
drwxr-xr-x.  13 root root  4096 Jul 18  2023 usr
drwxr-xr-x.  19 root root  4096 Jul 18  2023 var
[ATCG03@AIBIO03 /]$ cd /root
[ATCG03@AIBIO03 root]$ ll
total 144
-rwxr-xr-x   1 root root 98440 Sep 19  2023 bin
drwxr-xr-x   5 root root  4096 Jul 26 14:52 Database
-rw-r--r--   1 root root    16 Sep 26  2023 dnadist.cfg
drwxr-xr-x  30 root root  4096 Jul 28 19:06 Example
drwxr-xr-x   2 root root  4096 Sep 26  2023 __pycache__
drwxr-xr-x   3 root root  4096 Sep 25  2023 R
drwxr-xr-x 123 root root 20480 Jul 28 20:17 Software
[ATCG03@AIBIO03 root]$ cd Example/
[ATCG03@AIBIO03 Example]$ ll
total 112
drwxr-xr-x 13 197609 197609 4096 Sep 23  2023 darknet
drwxr-xr-x  4 root   root   4096 Sep 27  2023 deepcnv
drwxr-xr-x  3 root   root   4096 Sep 27  2023 Deepvariant_data
drwxr-xr-x  5 root   root   4096 Sep 25  2023 DNNGP-main
drwxr-xr-x 10 root   root   4096 Sep 25  2023 D-SCRIPT-main
drwxr-xr-x 11 root   root   4096 Jul 19 12:23 EPCOT-main
drwxr-xr-x  9 root   root   4096 Sep 26  2023 fusion_twas-master
drwxr-xr-x  4 root   root   4096 Sep 24  2023 Metagenome
drwxr-xr-x  7 root   root   4096 Sep 21  2023 ncov-Illumina
drwxr-xr-x 10 root   root   4096 Sep 24  2023 OmiEmbed-main
drwxr-xr-x  5 root   root   4096 Jul 28 19:17 pangenome
drwxr-xr-x  2 root   root   4096 Sep 27  2023 Population_Genetic_Evolution
drwxr-xr-x  7 root   root   4096 Sep 26  2023 pwas-master
drwxr-xr-x  8 root   root   4096 Sep 24  2023 quasildr-master
drwxr-xr-x  3 root   root   4096 Jul 26 17:10 reseq
drwxr-xr-x  2 root   root   4096 Jul 25 23:37 scDeepSort
drwxr-xr-x  3 root   root   4096 Jul 24 10:39 scPagwas
drwxr-xr-x  3 root   root   4096 Jul 30 16:02 scRNASeq_data
drwxr-xr-x 14 root   root   4096 Sep 25  2023 selene
drwxr-xr-x  7 root   root   4096 Sep 24  2023 Seq2Fun
drwxr-xr-x  5 root   root   4096 Jul 28 19:15 T2T
drwxr-xr-x 10 root   root   4096 Jul 26 00:46 TOSICA-main
drwxr-xr-x  3 root   root   4096 Sep 27  2023 TRUST4SRRexample
drwxr-xr-x  7 root   root   4096 Sep 26  2023 ukbb_parser
drwxr-xr-x  3 root   root   4096 Sep 26  2023 WEIGHTS
drwxr-xr-x  6 root   root   4096 Jul 28 21:24 WGBS
drwxr-xr-x  5 root   root   4096 Sep 26  2023 xinpian
drwxr-xr-x  5 root   root   4096 Sep 21  2023 XOmiVAE-main
[ATCG03@AIBIO03 Example]$ cd T2T
[ATCG03@AIBIO03 T2T]$ ll
total 12
drwxr-xr-x  2 root root 4096 Jul 28 15:25 data
drwxr-xr-x  5 root root 4096 Jul 26 14:55 database
drwxr-xr-x 15 root root 4096 Jul 28 19:12 myt2t
[ATCG03@AIBIO03 T2T]$ cd data
[ATCG03@AIBIO03 data]$ ll
total 18402468
-rwxr-xr-x 1 root root       9388 Jul 26 12:29 45s-rDNA.fa
-rwxr-xr-x 1 root root     529892 Jul 26 12:29 cp_mt.fasta
-rwxr-xr-x 1 root root 5606402340 Jul 26 14:11 hifi.fastq.gz
-rwxr-xr-x 1 root root 1740336432 Jul 26 14:13 illu_f1.fq.gz
-rwxr-xr-x 1 root root 1856523409 Jul 26 14:16 illu_r2.fq.gz
-rwxr-xr-x 1 root root 9505231165 Jul 26 14:51 ont.fastq.gz
-rwxr-xr-x 1 root root  135062572 Jul 26 12:30 ref.fasta

先将镜像上传至培训服务器

##查看现目前已有的镜像
[ATCG03@AIBIO03 data]$ docker images
REPOSITORY           TAG       IMAGE ID       CREATED         SIZE
bioi_pangenome       v1        4dc6870443e7   4 days ago      12.1GB
bioi_reseq           v1        24f90f5ade2e   5 days ago      8.86GB
bioi_t2t             v1        db4c10cba55a   5 days ago      17.8GB
pop-evol             v1.1      722503fbffa5   10 months ago   6.72GB
google/deepvariant   latest    45f6c7767ff0   17 months ago   6.98GB
##导入镜像
[ATCG03@AIBIO03 day3_t2t]$ docker load -i bioi_t2t_v1.tar
Loaded image: bioi_t2t:v1
##查看所有容器
[ATCG03@AIBIO03 day3_t2t]$ docker ps -a
CONTAINER ID   IMAGE                       COMMAND                  CREATED         STATUS                       PORTS     NAMES
221fddc288ce   bioi_reseq:v1               "sh -c /app/license/…"   4 days ago      Exited (0) 4 days ago                  inspiring_kepler
ad94f20b463f   bioi_reseq:v1               "sh -c /app/license/…"   4 days ago      Exited (0) 4 days ago                  bold_pasteur
ac3ff670ff07   a458ba9fc504                "sh -c /app/license/…"   5 days ago      Exited (2) 5 days ago                  exciting_sinoussi
cc36db3ee14c   a458ba9fc504                "sh -c /app/license/…"   5 days ago      Exited (0) 5 days ago                  compassionate_wescoff
f939a2967411   a458ba9fc504                "sh -c /app/license/…"   5 days ago      Exited (127) 5 days ago                sharp_goldwasser
2473e94e1744   6e3d468be98f                "/bin/bash"              5 days ago      Exited (130) 5 days ago                upbeat_liskov
408dce4b3e13   pop-evol:v1.1               "/bin/bash"              5 days ago      Exited (0) 5 days ago                  angry_liskov
73425f2e4549   google/deepvariant:latest   "/opt/deepvariant/bi…"   10 months ago   Exited (1) 10 months ago               nice_jackson
7aa482826fab   google/deepvariant          ": latest /opt/deepv…"   10 months ago   Created                                gallant_antonelli
c6e113f77f14   google/deepvariant:latest   "/opt/deepvariant/bi…"   10 months ago   Exited (0) 10 months ago               gracious_tharp
9f457b23d3d5   google/deepvariant:latest   "/opt/deepvariant/bi…"   10 months ago   Exited (0) 10 months ago               fervent_haslett
91f7c887e7e0   google/deepvariant:latest   "/opt/deepvariant/bi…"   10 months ago   Exited (1) 10 months ago               upbeat_ardinghelli
c558962d5dfc   google/deepvariant:latest   "/opt/deepvariant/bi…"   10 months ago   Exited (1) 10 months ago               thirsty_visvesvaraya
ceb7647052b0   6e3d468be98f                "bash"                   10 months ago   Exited (137) 10 months ago             strange_mcclintock
8554b6a851b8   6e3d468be98f                "bash"                   10 months ago   Created                                charming_colden
6585ee181186   6e3d468be98f                "bash"                   10 months ago   Created                                elegant_villani
32c53424f524   6e3d468be98f                "bash"                   10 months ago   Exited (0) 10 months ago               elastic_hodgkin
945df911eb2b   6e3d468be98f                "bash"                   10 months ago   Exited (1) 10 months ago               angry_turing
3070d809dad8   6e3d468be98f                "/bin/bash"              10 months ago   Exited (127) 10 months ago             peaceful_kapitsa
578d1a20cc6b   6e3d468be98f                "bash"                   10 months ago   Exited (137) 10 months ago             amazing_jemison
c4e69bec8e15   6e3d468be98f                "bash"                   10 months ago   Exited (1) 10 months ago               sweet_kare
f5a407a1774d   6e3d468be98f                "bash"                   10 months ago   Exited (1) 10 months ago               admiring_brattain
6fefc72ad2e8   6e3d468be98f                "bash"                   10 months ago   Exited (0) 10 months ago               eager_blackwell
6fcce9889813   722503fbffa5                "/bin/bash"              10 months ago   Exited (0) 10 months ago               inspiring_torvalds
0b9d26e699c5   6e3d468be98f                "/bin/bash"              10 months ago   Exited (0) 10 months ago               admiring_almeida

先传数据，再挂载文件
我之前是先挂载文件，再导入数据，所以我先把已经创建容器删掉

##退出当前容器
(base) [root@8ff8f3e79654  09:53:50 /]# exit
##停止容器
[ATCG03@AIBIO03 day3_t2t]$ docker stop py
py
##删除容器
[ATCG03@AIBIO03 day3_t2t]$ docker rm py
py

新建容器，并挂载到/home/ATCG03/day3_t2t/T2T/中，后续的输出结果都会在T2T目录下

[ATCG03@AIBIO03 day3_t2t]$ docker run -id -v /home/ATCG03/day3_t2t/T2T/:/work/T2T --name=py bioi_t2t:v1
b7395b3b4b8901fcecc3ec03c604c76c70ccb1a7f90b0af38ff94079845221aa
[ATCG03@AIBIO03 day3_t2t]$ docker ps -a
CONTAINER ID   IMAGE                       COMMAND                  CREATED             STATUS                       PORTS     NAMES
b7395b3b4b89   bioi_t2t:v1                 "sh -c /app/license/…"   11 seconds ago      Up 10 seconds                          py

####进入容器
[ATCG03@AIBIO03 day3_t2t]$ docker exec -it py /bin/bash
######################################################
#                   欢 迎 使 用                      #
#            基因组T2T组装分析docker镜像             #
######################################################

[root@b7395b3b4b89  13:26:16 /work]#