diff --git a/.doctrees/course_contents/HandsOn.doctree b/.doctrees/course_contents/HandsOn.doctree index 2a6384e..bcb4f32 100644 Binary files a/.doctrees/course_contents/HandsOn.doctree and b/.doctrees/course_contents/HandsOn.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index ebf482b..0de7e07 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/_sources/course_contents/HandsOn.md b/_sources/course_contents/HandsOn.md index c74ffb1..126bacf 100644 --- a/_sources/course_contents/HandsOn.md +++ b/_sources/course_contents/HandsOn.md @@ -1,4 +1,52 @@ # Docker Hands-on beginners training -Inspired on Nextflow training: +Inspired by Nextflow training: +In this hands on, we assume you already have an environment with docker installed, either locally, or remotely in a place such as github codespaces which we have made ready for you in this occation. + +Once the docker daemon is running you can run containers, we will start with the `hello-world` container, which is hosted on Docker Hub. + +In your command line, a docker container can be run with the following syntax: +``` +docker run +``` + +Excercise: + +Run the publicly available `hello-world` container. + +Solution: + +``` +docker run hello-world +``` + + + +We notice that docker first tried to check if we had the container locally, as we did not, the online container repositories were checked. +As the container was found, it was donwloaded, and run. + +We can also break down the step and only download an image without running it. This is done with the `pull` command using the following syntax: +``` +docker pull +``` + +To check which containers you have pulled, you can use `images` with the following syntax: +``` +docker images +``` + + + + + +Excercise: + +Pull the publicly available `debian:bullseye-slim` container and verify it has been downloaded + +Solution: + +``` +docker pull debian:bullseye-slim +docker images +``` diff --git a/course_contents/HandsOn.html b/course_contents/HandsOn.html index 978ed4a..ac93bb7 100644 --- a/course_contents/HandsOn.html +++ b/course_contents/HandsOn.html @@ -336,7 +336,36 @@

Docker Hands-on beginners training

Docker Hands-on beginners training#

-

Inspired on Nextflow training: https://training.nextflow.io/basic_training/containers/

+

Inspired by Nextflow training: https://training.nextflow.io/basic_training/containers/

+

In this hands on, we assume you already have an environment with docker installed, either locally, or remotely in a place such as github codespaces which we have made ready for you in this occation.

+

Once the docker daemon is running you can run containers, we will start with the hello-world container, which is hosted on Docker Hub.

+

In your command line, a docker container can be run with the following syntax:

+
docker run <container-name>
+
+
+

Excercise:

+

Run the publicly available hello-world container.

+

Solution:

+
docker run hello-world
+
+
+

We notice that docker first tried to check if we had the container locally, as we did not, the online container repositories were checked. +As the container was found, it was donwloaded, and run.

+

We can also break down the step and only download an image without running it. This is done with the pull command using the following syntax:

+
docker pull <container-name>
+
+
+

To check which containers you have pulled, you can use images with the following syntax:

+
docker images
+
+
+

Excercise:

+

Pull the publicly available debian:bullseye-slim container and verify it has been downloaded

+

Solution:

+
docker pull debian:bullseye-slim
+docker images
+
+
diff --git a/searchindex.js b/searchindex.js index 21f549b..5c22f36 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"About": [[0, null], [0, "id1"]], "Container images repositories": [[7, "container-images-repositories"]], "Data Science platform": [[0, "data-science-platform"]], "Docker": [[3, "docker"]], "Docker Hands-on beginners training": [[2, null]], "Docker Introduction": [[1, null], [6, null]], "Docker desktop installation link": [[7, "docker-desktop-installation-link"]], "Instructions": [[3, null]], "Location": [[4, null]], "Objectives": [[0, "objectives"]], "Opening the Github codespace to have an environment to work with the Docker": [[3, "opening-the-github-codespace-to-have-an-environment-to-work-with-the-docker"]], "Resources": [[7, null]], "The course": [[0, "the-course"]], "Timing": [[5, null]]}, "docnames": ["about", "course_contents/DockerIntro", "course_contents/HandsOn", "course_information/Instructions", "course_information/Location", "course_information/Timing", "index", "resources"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.md", "course_contents/DockerIntro.md", "course_contents/HandsOn.md", "course_information/Instructions.md", "course_information/Location.md", "course_information/Timing.md", "index.md", "resources.md"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": 6, "00": 5, "002": 4, "10": 5, "11": 5, "12": 5, "19th": [4, 5], "2": 6, "2025": [4, 5], "208": [4, 5], "30": 5, "A": 5, "And": 6, "As": 0, "If": 3, "In": 0, "It": 3, "The": 4, "There": 3, "These": 1, "To": 3, "about": [3, 4], "academia": 0, "acceler": 0, "accept": 3, "access": 0, "account": 1, "across": 0, "ad": [0, 3], "addit": 3, "address": 1, "after": 3, "agenda": 5, "aim": 0, "alc3": 4, "all": 6, "also": 0, "alwai": 6, "an": 0, "analyt": 0, "approach": 0, "ar": [1, 3], "ask": 6, "autom": 0, "automat": 3, "avoid": 3, "base": 0, "basic_train": 2, "becaus": 1, "becom": 0, "best": 0, "between": 1, "bioengin": 0, "bioinformat": [1, 6], "biologi": [0, 6], "biosustain": 0, "both": 0, "build": [1, 4, 5], "built": 3, "button": 3, "campu": 4, "can": [0, 1, 6], "central": [0, 1], "centric": 0, "challeng": 1, "chang": 3, "class": [3, 5], "click": 3, "club": [0, 4, 5, 6], "code": 3, "collabor": [0, 1], "common": 1, "commun": 0, "compar": 6, "comput": [0, 6], "configur": 3, "consum": 3, "contact": [0, 6], "contain": [0, 1, 2, 3, 6], "control": 1, "coorgan": 0, "cours": 3, "creat": [0, 3], "credit": 3, "custom": 3, "dai": 3, "data": [4, 5, 6], "dataset": 0, "default": 3, "delet": 3, "depend": [1, 3, 6], "deploi": 3, "design": 0, "desktop": 1, "devcontain": 3, "differ": 1, "directli": 3, "do": 3, "docker": [0, 4], "dockerfil": [0, 3], "don": 3, "download": 3, "dsp": 0, "dtu": [0, 4], "dure": 6, "e": [1, 3], "each": 0, "educ": 0, "email": [0, 6], "end": 3, "ensur": 6, "entir": 0, "environ": 1, "essenti": [0, 6], "evolv": 0, "extens": 3, "februari": [4, 5], "fellow": 0, "field": 1, "figur": 6, "file": [0, 3], "first": 0, "focus": 0, "follow": [0, 3], "four": 0, "free": 3, "g": 1, "gain": 0, "gener": 0, "go": 3, "ha": 0, "hall": 5, "hand": 5, "handi": 1, "her": 6, "here": [0, 3], "high": 0, "him": 6, "host": 1, "how": 0, "http": 2, "hub": [0, 1, 7], "i": [0, 1, 3, 4, 5, 6], "imag": 1, "imagein": 0, "implement": 0, "imposs": 6, "inclus": 0, "industri": 0, "inform": 0, "infrastructur": 0, "innov": 0, "insight": 0, "inspir": 2, "instal": [0, 1, 3, 6], "integr": [0, 1], "interact": 0, "introduc": 0, "introduct": 5, "involv": 0, "io": 2, "issu": 3, "json": 3, "known": 1, "learn": [0, 3], "level": 0, "lifecycl": 0, "like": 6, "link": 3, "login": 0, "lot": 1, "lunch": [5, 6], "machin": [0, 6], "mainten": 1, "make": [0, 6], "manag": [1, 6], "mandatori": 1, "manual": 3, "match": 3, "method": 0, "mind": 0, "more": [0, 3], "mount": 0, "move": 5, "multidisciplinari": 0, "need": [0, 6], "network": 5, "new": 0, "nextflow": [1, 2, 3], "nice": 6, "now": 3, "number": 6, "o": 3, "occupi": 1, "one": 0, "ongo": 0, "onli": 0, "open": 0, "option": 3, "organ": 0, "other": 1, "our": 0, "out": 6, "output": 0, "over": 6, "pai": 3, "parti": 1, "piec": 0, "pillar": 0, "pipelin": 6, "place": 6, "platform": 6, "pleas": 3, "portabl": [1, 6], "practic": 0, "pre": 6, "process": 0, "product": 0, "program": 0, "project": 0, "promot": 0, "provid": 0, "publish": 1, "pull": 0, "pursu": 0, "q": 5, "quai": [1, 7], "question": 6, "rather": 0, "re": 3, "realet": 0, "rememb": [3, 6], "repositori": [1, 3], "reproduc": [1, 6], "requir": 0, "research": 0, "result": 6, "reusag": 0, "review": 6, "rnaseq": 0, "room": 4, "run": [0, 1], "sai": 3, "save": 1, "scalabl": 1, "scienc": 6, "send": 6, "session": 4, "sever": 1, "share": 1, "simplifi": 6, "so": 3, "softwar": [0, 6], "sofwar": 1, "some": 0, "sound": 6, "sourc": 0, "specif": 3, "standard": 0, "statist": 0, "strategi": 0, "support": 0, "system": 0, "t": [3, 6], "tab": 3, "take": 1, "team": 0, "technologi": 0, "tediou": 6, "tell": 6, "text": 0, "than": 0, "thei": 1, "them": 6, "thi": [0, 1, 3, 5], "thing": 1, "time": 0, "tool": [0, 1], "u": [0, 6], "ubuntu": 3, "up": 6, "upload": [0, 1], "us": 1, "usag": 0, "v": 3, "veri": 6, "version": [1, 3, 6], "vscode": 3, "want": 3, "we": [0, 3, 5], "websit": 3, "what": [0, 6], "when": 1, "where": 1, "which": 6, "while": 0, "why": 0, "wide": 1, "work": [0, 6], "workflow": 6, "workshop": 0, "worth": 1, "wouldn": 6, "you": [0, 1, 3, 6], "your": [0, 3, 6]}, "titles": ["About", "Docker Introduction", "Docker Hands-on beginners training", "Instructions", "Location", "Timing", "Docker Introduction", "Resources"], "titleterms": {"The": 0, "about": 0, "an": 3, "beginn": 2, "codespac": 3, "contain": 7, "cours": 0, "data": 0, "desktop": 7, "docker": [1, 2, 3, 6, 7], "environ": 3, "github": 3, "hand": 2, "have": 3, "imag": 7, "instal": 7, "instruct": 3, "introduct": [1, 6], "link": 7, "locat": 4, "object": 0, "open": 3, "platform": 0, "repositori": 7, "resourc": 7, "scienc": 0, "time": 5, "train": 2, "work": 3}}) \ No newline at end of file +Search.setIndex({"alltitles": {"About": [[0, null], [0, "id1"]], "Container images repositories": [[7, "container-images-repositories"]], "Data Science platform": [[0, "data-science-platform"]], "Docker": [[3, "docker"]], "Docker Hands-on beginners training": [[2, null]], "Docker Introduction": [[1, null], [6, null]], "Docker desktop installation link": [[7, "docker-desktop-installation-link"]], "Instructions": [[3, null]], "Location": [[4, null]], "Objectives": [[0, "objectives"]], "Opening the Github codespace to have an environment to work with the Docker": [[3, "opening-the-github-codespace-to-have-an-environment-to-work-with-the-docker"]], "Resources": [[7, null]], "The course": [[0, "the-course"]], "Timing": [[5, null]]}, "docnames": ["about", "course_contents/DockerIntro", "course_contents/HandsOn", "course_information/Instructions", "course_information/Location", "course_information/Timing", "index", "resources"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.md", "course_contents/DockerIntro.md", "course_contents/HandsOn.md", "course_information/Instructions.md", "course_information/Location.md", "course_information/Timing.md", "index.md", "resources.md"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": 6, "00": 5, "002": 4, "10": 5, "11": 5, "12": 5, "19th": [4, 5], "2": 6, "2025": [4, 5], "208": [4, 5], "30": 5, "A": 5, "And": 6, "As": [0, 2], "If": 3, "In": [0, 2], "It": 3, "The": 4, "There": 3, "These": 1, "To": [2, 3], "about": [3, 4], "academia": 0, "acceler": 0, "accept": 3, "access": 0, "account": 1, "across": 0, "ad": [0, 3], "addit": 3, "address": 1, "after": 3, "agenda": 5, "aim": 0, "alc3": 4, "all": 6, "alreadi": 2, "also": [0, 2], "alwai": 6, "an": [0, 2], "analyt": 0, "approach": 0, "ar": [1, 3], "ask": 6, "assum": 2, "autom": 0, "automat": 3, "avail": 2, "avoid": 3, "base": 0, "basic_train": 2, "becaus": 1, "becom": 0, "been": 2, "best": 0, "between": 1, "bioengin": 0, "bioinformat": [1, 6], "biologi": [0, 6], "biosustain": 0, "both": 0, "break": 2, "build": [1, 4, 5], "built": 3, "bullsey": 2, "button": 3, "campu": 4, "can": [0, 1, 2, 6], "central": [0, 1], "centric": 0, "challeng": 1, "chang": 3, "check": 2, "class": [3, 5], "click": 3, "club": [0, 4, 5, 6], "code": 3, "codespac": 2, "collabor": [0, 1], "command": 2, "common": 1, "commun": 0, "compar": 6, "comput": [0, 6], "configur": 3, "consum": 3, "contact": [0, 6], "contain": [0, 1, 2, 3, 6], "control": 1, "coorgan": 0, "cours": 3, "creat": [0, 3], "credit": 3, "custom": 3, "daemon": 2, "dai": 3, "data": [4, 5, 6], "dataset": 0, "debian": 2, "default": 3, "delet": 3, "depend": [1, 3, 6], "deploi": 3, "design": 0, "desktop": 1, "devcontain": 3, "did": 2, "differ": 1, "directli": 3, "do": 3, "docker": [0, 4], "dockerfil": [0, 3], "don": 3, "done": 2, "donwload": 2, "down": 2, "download": [2, 3], "dsp": 0, "dtu": [0, 4], "dure": 6, "e": [1, 3], "each": 0, "educ": 0, "either": 2, "email": [0, 6], "end": 3, "ensur": 6, "entir": 0, "environ": [1, 2], "essenti": [0, 6], "evolv": 0, "excercis": 2, "extens": 3, "februari": [4, 5], "fellow": 0, "field": 1, "figur": 6, "file": [0, 3], "first": [0, 2], "focus": 0, "follow": [0, 2, 3], "found": 2, "four": 0, "free": 3, "g": 1, "gain": 0, "gener": 0, "github": 2, "go": 3, "ha": [0, 2], "had": 2, "hall": 5, "hand": 5, "handi": 1, "have": 2, "hello": 2, "her": 6, "here": [0, 3], "high": 0, "him": 6, "host": [1, 2], "how": 0, "http": 2, "hub": [0, 1, 2, 7], "i": [0, 1, 2, 3, 4, 5, 6], "imag": [1, 2], "imagein": 0, "implement": 0, "imposs": 6, "inclus": 0, "industri": 0, "inform": 0, "infrastructur": 0, "innov": 0, "insight": 0, "inspir": 2, "instal": [0, 1, 2, 3, 6], "integr": [0, 1], "interact": 0, "introduc": 0, "introduct": 5, "involv": 0, "io": 2, "issu": 3, "json": 3, "known": 1, "learn": [0, 3], "level": 0, "lifecycl": 0, "like": 6, "line": 2, "link": 3, "local": 2, "login": 0, "lot": 1, "lunch": [5, 6], "machin": [0, 6], "made": 2, "mainten": 1, "make": [0, 6], "manag": [1, 6], "mandatori": 1, "manual": 3, "match": 3, "method": 0, "mind": 0, "more": [0, 3], "mount": 0, "move": 5, "multidisciplinari": 0, "name": 2, "need": [0, 6], "network": 5, "new": 0, "nextflow": [1, 2, 3], "nice": 6, "notic": 2, "now": 3, "number": 6, "o": 3, "occat": 2, "occupi": 1, "onc": 2, "one": 0, "ongo": 0, "onli": [0, 2], "onlin": 2, "open": 0, "option": 3, "organ": 0, "other": 1, "our": 0, "out": 6, "output": 0, "over": 6, "pai": 3, "parti": 1, "piec": 0, "pillar": 0, "pipelin": 6, "place": [2, 6], "platform": 6, "pleas": 3, "portabl": [1, 6], "practic": 0, "pre": 6, "process": 0, "product": 0, "program": 0, "project": 0, "promot": 0, "provid": 0, "publicli": 2, "publish": 1, "pull": [0, 2], "pursu": 0, "q": 5, "quai": [1, 7], "question": 6, "rather": 0, "re": 3, "readi": 2, "realet": 0, "rememb": [3, 6], "remot": 2, "repositori": [1, 2, 3], "reproduc": [1, 6], "requir": 0, "research": 0, "result": 6, "reusag": 0, "review": 6, "rnaseq": 0, "room": 4, "run": [0, 1, 2], "sai": 3, "save": 1, "scalabl": 1, "scienc": 6, "send": 6, "session": 4, "sever": 1, "share": 1, "simplifi": 6, "slim": 2, "so": 3, "softwar": [0, 6], "sofwar": 1, "solut": 2, "some": 0, "sound": 6, "sourc": 0, "specif": 3, "standard": 0, "start": 2, "statist": 0, "step": 2, "strategi": 0, "support": 0, "syntax": 2, "system": 0, "t": [3, 6], "tab": 3, "take": 1, "team": 0, "technologi": 0, "tediou": 6, "tell": 6, "text": 0, "than": 0, "thei": 1, "them": 6, "thi": [0, 1, 2, 3, 5], "thing": 1, "time": 0, "tool": [0, 1], "tri": 2, "u": [0, 6], "ubuntu": 3, "up": 6, "upload": [0, 1], "us": [1, 2], "usag": 0, "v": 3, "veri": 6, "verifi": 2, "version": [1, 3, 6], "vscode": 3, "wa": 2, "want": 3, "we": [0, 2, 3, 5], "websit": 3, "were": 2, "what": [0, 6], "when": 1, "where": 1, "which": [2, 6], "while": 0, "why": 0, "wide": 1, "without": 2, "work": [0, 6], "workflow": 6, "workshop": 0, "world": 2, "worth": 1, "wouldn": 6, "you": [0, 1, 2, 3, 6], "your": [0, 2, 3, 6]}, "titles": ["About", "Docker Introduction", "Docker Hands-on beginners training", "Instructions", "Location", "Timing", "Docker Introduction", "Resources"], "titleterms": {"The": 0, "about": 0, "an": 3, "beginn": 2, "codespac": 3, "contain": 7, "cours": 0, "data": 0, "desktop": 7, "docker": [1, 2, 3, 6, 7], "environ": 3, "github": 3, "hand": 2, "have": 3, "imag": 7, "instal": 7, "instruct": 3, "introduct": [1, 6], "link": 7, "locat": 4, "object": 0, "open": 3, "platform": 0, "repositori": 7, "resourc": 7, "scienc": 0, "time": 5, "train": 2, "work": 3}}) \ No newline at end of file