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	<title><![CDATA[BOL: Basic docker commands !]]></title>
	<link>https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands?</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands</guid>
	<pubDate>Wed, 18 Mar 2020 07:33:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands</link>
	<title><![CDATA[Basic docker commands !]]></title>
	<description><![CDATA[<code>jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system df
TYPE                TOTAL               ACTIVE              SIZE                RECLAIMABLE
Images              47                  39                  3.701GB             3.177GB (85%)
Containers          121                 0                   1.513GB             1.513GB (100%)
Local Volumes       0                   0                   0B                  0B
Build Cache         0                   0                   0B                  0B
jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system prune
WARNING! This will remove:
  - all stopped containers
  - all networks not used by at least one container
  - all dangling images
  - all dangling build cache

Are you sure you want to continue? [y/N] y
Deleted Containers:
0b523b97fd6d70456bad5843147ec3f5c069c20cc1d7048ce78202058b63b2a6
9d6d29988baa09b2f1a1745de448896d2820ba52f9927497d5a1d433cb01c61a
5baf6ec5bb11291090b386ad85574a64db7bbb7a01d504e6d6174a80e05628bb

Deleted Images:
deleted: sha256:a62df23989f7419cfb04d9fee7fee8c6dcf548bbb0af6a63bd02d5629f2189f8
deleted: sha256:d8c4b90ecbd8d3ad6a09a34c5880d9d68233ec2e5760a630684e1012eaf4ded6
deleted: sha256:85a4247b883f9cc31cb59e93f135d243837190bcd010b626604895fa8f20dcec

Total reclaimed space: 2.049GB
jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system df
TYPE                TOTAL               ACTIVE              SIZE                RECLAIMABLE
Images              9                   0                   3.165GB             3.165GB (100%)
Containers          0                   0                   0B                  0B
Local Volumes       0                   0                   0B                  0B
Build Cache         0                   0                   0B                  0B
jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker build -t mydocker .
Sending build context to Docker daemon  9.023MB
Step 1/12 : FROM ubuntu:14.04
 ---&gt; 6e4f1fe62ff1
Step 2/12 : FROM perl:latest
 ---&gt; 82330051f9cb
Step 3/12 : FROM bioperl/bioperl-deps
 ---&gt; e890cc223da3
Step 4/12 : MAINTAINER &quot;Jitendra Narayan&quot; &lt;jnarayan81@gmail.com&gt;
 ---&gt; Using cache
 ---&gt; 13519702cbe1
Step 5/12 : RUN apt-get update --yes &amp;&amp;     apt-get install --yes git
 ---&gt; Using cache
 ---&gt; 0974217c0b0e
Step 6/12 : RUN apt-get install --yes   build-essential   gcc-multilib   perl
 ---&gt; Using cache
 ---&gt; 96d284c0408b
Step 7/12 : RUN apt-get install -y bioperl &amp;&amp;     apt-get install -y libstatistics-distributions-perl &amp;&amp;     apt-get install -y libterm-progressbar-simple-perl &amp;&amp;     apt-get install -y libbio-scf-perl
 ---&gt; Using cache
 ---&gt; 3509d5eb05a5
Step 8/12 : RUN apt-get install -y curl &amp;&amp;     cpan install App::cpanminus
 ---&gt; Using cache
 ---&gt; e79748ebdffd
Step 9/12 : RUN cpanm install File::chdir &amp;&amp;     cpanm install lib::abs &amp;&amp;     cpanm install File::Remove &amp;&amp;     cpanm install Spreadsheet::Read &amp;&amp;     cpanm install Statistics::ChiSquare
 ---&gt; Using cache
 ---&gt; d34787da52e0
Step 10/12 : WORKDIR home/
 ---&gt; Using cache
 ---&gt; d1ba7714283f
Step 11/12 : COPY autoConTAMPR home/
 ---&gt; Using cache
 ---&gt; cc3fe61a6e14
Step 12/12 : ENTRYPOINT [&quot;perl&quot;, &quot;home/bin/autoConTAMPR.pl&quot;]
 ---&gt; Using cache
 ---&gt; 4a2cc5876794
Successfully built 4a2cc5876794
Successfully tagged mydocker:latest
jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker run mydocker

  --.---. .-. .---
	 / \
	/ ^ \
  --autoConTAMPR v0.1--

Citation - autoConTAMPR: Automatic Contingency Table Analysis of Minority Peak Ranks
License: Creative Commons Licence
Bug-reports and requests to: https://github.com/jnarayan81/autoConTAMPR/issues

Operating system: linux
Perl executable at: /usr/bin/perl

Please check manual.
Usage:
    autoConTAMPR.pl --validate/-v

            autoConTAMPR.pl --validate/-v --conf/-c &lt;configuration file&gt;

    autoConTAMPR.pl --plot/-p

            autoConTAMPR.pl --plot/-p --conf/-c &lt;configuration file&gt;

    autoConTAMPR.pl --install/-i

            autoConTAMPR.pl --install/-i --conf/-c &lt;configuration file&gt;

jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system info
Client:
 Debug Mode: false

Server:
 Containers: 1
  Running: 0
  Paused: 0
  Stopped: 1
 Images: 17
 Server Version: 19.03.8
 Storage Driver: overlay2
  Backing Filesystem: &lt;unknown&gt;
  Supports d_type: true
  Native Overlay Diff: true
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: runc
 Default Runtime: runc
 Init Binary: docker-init
 init version: fec3683
 Security Options:
  apparmor
  seccomp
   Profile: default
 Kernel Version: 4.15.0-88-generic
 Operating System: Ubuntu 18.04.4 LTS
 OSType: linux
 Architecture: x86_64
 CPUs: 2
 Total Memory: 3.594GiB
 Name: jit-HP-Pro-3335-MTL
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

WARNING: No swap limit support</code>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink='true'>https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands#item-annotation-3988</guid>
	<pubDate>Mon, 06 Sep 2021 04:38:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands#item-annotation-3988</link>
	<title><![CDATA[Comment by Jit]]></title>
	<description><![CDATA[<p>Start the docker container</p>
<p><span>docker start [options] container_id </span></p>
<p>Stop the docker container</p>
<p><span>docker stop --time=20 container_id</span></p>
<p><span>Kill a docker container</span></p>
<p><span><span>docker kill [option] container_id</span></span></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink='true'>https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands#item-annotation-3987</guid>
	<pubDate>Mon, 06 Sep 2021 04:16:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands#item-annotation-3987</link>
	<title><![CDATA[Comment by Jit]]></title>
	<description><![CDATA[<p>Attached the running docker&nbsp;</p>
<p>Instead of using&nbsp;<span><code>-i</code>&nbsp;</span>or<span>&nbsp;<code>-t</code></span>&nbsp;options, use the&nbsp;<a href="https://phoenixnap.com/kb/how-to-ssh-into-docker-container"><span><code>attach</code></span>&nbsp;command to connect to a running container</a>:</p>
<pre><code>docker attach container_id</code></pre>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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