From 3f34fa911f93c2dc7272d7b3b55d2fc4ce1b9fcc Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 10 Oct 2023 10:22:45 +0000 Subject: [PATCH] Add changes for 638bc8eb52dbb5d861b1addcfdfbafe1577d1950 --- _sources/docker.rst.txt | 2 +- docker.html | 2 +- searchindex.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/_sources/docker.rst.txt b/_sources/docker.rst.txt index cfd1eb4..6a7981c 100644 --- a/_sources/docker.rst.txt +++ b/_sources/docker.rst.txt @@ -313,7 +313,7 @@ Volume exercises docker run --user ----------------- -It is possible to run certain containers with a specific user, appending ```run --user```. +It is possible to run some containers with a specific user, appending ```run --user```. A convenient command would be: diff --git a/docker.html b/docker.html index 514c889..4e6e98b 100644 --- a/docker.html +++ b/docker.html @@ -321,7 +321,7 @@

Volume exercises

docker run –user

-

It is possible to run certain containers with a specific user, appending `run --user`.

+

It is possible to run some containers with a specific user, appending `run --user`.

A convenient command would be:

docker run --user $(id -u):$(id -g) --detach --volume $(pwd)/test:/scratch --name user_test biocontainers/fastqc:v0.11.9_cv7 touch /scratch/userfile
diff --git a/searchindex.js b/searchindex.js index 7453c66..737e99d 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["containers", "docker", "docker_2", "index", "singularity"], "filenames": ["containers.rst", "docker.rst", "docker_2.rst", "index.rst", "singularity.rst"], "titles": ["Containers", "Docker", "Docker 2", "Scientific Containers CRG PhD course 2023", "Singularity"], "terms": {"A": [0, 1, 2], "can": [0, 1, 2, 4], "seen": 0, "minim": 0, "environ": [0, 1, 2], "us": [0, 2, 4], "ani": [0, 1], "compat": [0, 1], "beyond": 0, "i": [0, 2, 4], "time": [0, 4], "resourc": 0, "save": [0, 2], "thei": [0, 1, 4], "allow": 0, "control": 0, "softwar": [0, 1, 4], "instal": 0, "depend": [0, 2, 4], "reproduc": [0, 4], "analysi": 0, "u": [0, 1], "exactli": 0, "same": [0, 1, 2], "version": [0, 1, 2, 4], "tool": [0, 1, 4], "virtualis": 0, "containeris": 0, "aka": 0, "lightweight": 0, "abstract": 0, "physic": 0, "hardwar": 0, "applic": [0, 1], "layer": [0, 1, 2], "hypervisor": 0, "host": [0, 1, 2, 4], "kernel": 0, "o": 0, "do": [0, 1], "confus": [0, 4], "emul": 0, "bundl": 0, "all": [0, 1, 2, 4], "togeth": 0, "enabl": 0, "everi": [0, 2], "an": [0, 1, 2, 4], "oper": [0, 2], "system": [0, 1, 2, 4], "sourc": [0, 2, 4], "pro": [0, 1, 4], "con": 0, "adv": 0, "veri": 0, "similar": [0, 4], "full": 0, "high": [0, 1, 4], "divers": 0, "No": [0, 4], "need": [0, 4], "less": 0, "space": [0, 1], "better": 0, "portabl": [0, 4], "faster": 0, "than": 0, "easier": 0, "autom": 0, "distribut": 0, "recip": [0, 1], "more": [0, 1, 4], "slower": 0, "Not": 0, "good": [0, 2, 4], "some": [0, 1, 2, 4], "case": [0, 1, 2], "might": [0, 4], "still": 0, "even": [0, 2], "current": [0, 1, 2], "solut": [0, 2, 4], "platform": 1, "develop": [1, 4], "ship": 1, "infrastructur": 1, "code": 1, "first": [1, 2, 4], "2013": 1, "compani": 1, "origin": [1, 4], "dotcloud": 1, "2010": 1, "later": [1, 4], "name": [1, 2, 4], "establish": 1, "open": 1, "initi": [1, 4], "As": [1, 2], "commun": 1, "edit": [1, 4], "enterpris": 1, "There": 1, "increas": 1, "number": [1, 2], "altern": 1, "technologi": 1, "provid": [1, 4], "mani": 1, "them": [1, 4], "ar": [1, 2, 4], "base": [1, 2], "from": [1, 2, 4], "stack": 1, "usual": 1, "try": [1, 2], "address": 1, "specif": [1, 2], "weak": [1, 4], "point": [1, 4], "exampl": [1, 2, 4], "singular": [1, 3], "which": [1, 2, 4], "we": [1, 2, 4], "introduc": 1, "thi": [1, 2, 4], "cours": 1, "focus": [1, 4], "hpc": [1, 4], "anoth": [1, 2], "http": [1, 2, 4], "io": [1, 2], "__": 1, "keep": 1, "function": [1, 4], "differ": [1, 2, 4], "focu": [1, 4], "daemon": [1, 4], "permiss": [1, 4], "command": [1, 4], "alia": 1, "our": 1, "read": [1, 4], "onli": [1, 2, 4], "templat": 1, "have": [1, 2, 4], "sever": 1, "set": [1, 2], "inert": 1, "instanc": [1, 2, 4], "call": [1, 2], "when": [1, 2, 4], "you": [1, 2, 4], "The": [1, 2, 4], "cake": 1, "make": [1, 2], "like": 1, "given": [1, 2], "stackoverflow": 1, "com": [1, 2, 4], "question": [1, 2], "23735149": 1, "between": [1, 2], "place": [1, 4], "follow": [1, 2], "bit": 1, "config": 1, "storag": 1, "conf": [1, 4], "driver": 1, "overlai": 1, "graphroot": 1, "tmp": [1, 4], "local": [1, 2, 4], "share": [1, 4], "option": [1, 2, 4], "mount_program": 1, "usr": [1, 2, 4], "bin": [1, 2, 4], "fuse": 1, "overlayf": 1, "get": [1, 2], "help": [1, 4], "store": [1, 4], "registri": 1, "main": [1, 4], "public": [1, 4], "let": [1, 2, 4], "": [1, 2, 4], "search": 1, "keyword": 1, "ubuntu": [1, 2], "latest": [1, 2], "releas": 1, "choos": 1, "fetch": 1, "tag": 1, "22": 1, "04": [1, 2], "directori": [1, 2], "bioinformat": [1, 4], "relat": 1, "entri": 1, "quai": 1, "redhat": 1, "normal": [1, 4], "creat": [1, 4], "bioconda": [1, 2], "fastqc": [1, 4], "v0": [1, 4], "11": [1, 4], "9_cv7": [1, 4], "each": [1, 2], "ha": 1, "uniqu": 1, "id": [1, 2], "now": [1, 4], "want": 1, "insid": [1, 2, 4], "fresh": 1, "activ": 1, "static": 1, "format": 1, "l": [1, 4], "your": [1, 4], "work": [1, 2, 4], "result": [1, 2], "program": [1, 2, 4], "whoami": 1, "cat": 1, "etc": [1, 2, 4], "issu": [1, 4], "either": 1, "line": [1, 2, 4], "see": [1, 2], "abov": 1, "interact": 1, "enter": 1, "bash": [1, 2, 4], "background": 1, "detach": 1, "tail": 1, "f": [1, 2, 4], "dev": [1, 2], "null": 1, "myubuntu": 1, "whether": 1, "unam": 1, "df": 1, "remov": [1, 4], "unus": 1, "other": [1, 4], "WITH": 1, "care": 1, "prune": 1, "non": 1, "much": 1, "refer": 1, "www": 1, "digitalocean": 1, "tutori": [1, 2], "how": [1, 4], "fulli": 1, "isol": [1, 4], "It": [1, 2, 4], "necessari": 1, "mount": [1, 4], "order": [1, 2], "handl": 1, "input": 1, "output": [1, 2], "file": [1, 2, 4], "syntax": [1, 2, 4], "v": 1, "mkdir": [1, 2, 4], "test": [1, 4], "touch": [1, 4], "pwd": [1, 4], "scratch": [1, 4], "fastqc_contain": 1, "ti": [1, 4], "exit": [1, 4], "copi": [1, 2, 4], "2": [1, 3, 4], "fastq": [1, 4], "avail": [1, 2, 4], "dataset": 1, "github": [1, 3], "repositori": [1, 2, 3, 4], "gz": [1, 4], "outsid": [1, 4], "possibl": 1, "certain": 1, "append": 1, "conveni": [1, 4], "would": [1, 2, 4], "g": [1, 2, 4], "user_test": 1, "userfil": 1, "underli": 2, "wai": [2, 4], "know": 2, "popular": [2, 4], "ones": [2, 4], "debian": 2, "cento": 2, "alpin": 2, "conda": 2, "anaconda": 2, "forg": 2, "In": 2, "apt": 2, "y": 2, "yum": 2, "check": [2, 4], "libxml2": 2, "devel": 2, "x86_64": 2, "note": [2, 4], "br": 2, "import": 2, "context": 2, "mean": 2, "answer": 2, "ye": 2, "regard": 2, "should": 2, "text": 2, "default": [2, 4], "dockerfil": 2, "row": 2, "correspond": 2, "final": 2, "parent": 2, "typic": 2, "18": 2, "run": 2, "execut": 2, "filesystem": [2, 4], "think": 2, "about": 2, "essenti": 2, "what": [2, 4], "freshli": 2, "wget": 2, "implicit": 2, "look": 2, "stand": 2, "process": [2, 4], "sens": 2, "avoid": [2, 4], "overpopul": 2, "actual": 2, "defin": 2, "dure": 2, "t": [2, 4], "imagenam": 2, "If": [2, 4], "mytestimag": 2, "over": 2, "popul": 2, "inspect": 2, "includ": 2, "e": [2, 4], "dockerignor": 2, "specifi": 2, "path": 2, "inform": [2, 4], "codefresh": 2, "ignor": 2, "last": [2, 4], "successfulli": 2, "built": 2, "go": 2, "newli": 2, "list": 2, "Then": 2, "f9f41698e2f8": 2, "workdir": 2, "subsequ": 2, "action": 2, "add": 2, "explain": 2, "here": [2, 4], "machin": 2, "also": [2, 4], "url": 2, "tar": 2, "archiv": 2, "automat": 2, "extract": 2, "upon": 2, "being": 2, "sai": 2, "jpg": 2, "destin": 2, "sophist": 2, "p": 2, "data": [2, 4], "env": [2, 4], "arg": 2, "variabl": [2, 4], "valu": 2, "while": 2, "futur": 2, "contain": 2, "cmd": 2, "entrypoint": 2, "gener": [2, 4], "start": 2, "alwai": 2, "argument": 2, "fed": 2, "below": 2, "without": [2, 4], "echo": 2, "hello": 2, "world": [2, 4], "moon": 2, "complex": 2, "maintain": 2, "toni": 2, "hermoso": 2, "pulido": 2, "crg": 2, "eu": 2, "cdn": 2, "wp": 2, "nginx": 2, "content": [2, 3, 4], "upload": 2, "2016": [2, 4], "07": 2, "swarm": 2, "hero2": 2, "png": 2, "1": [2, 4], "medium": 2, "max": 2, "1600": 2, "_nqn6_ynxs29m8vfzwyleg": 2, "To": 2, "e23aaea5dff1": 2, "ubuntu_wget": 2, "0": [2, 4], "random": 2, "short": 2, "script": 2, "random_numb": 2, "seq": 2, "1000": 2, "shuf": 2, "head": 2, "interg": 2, "integ": 2, "select": 2, "write": [2, 4], "7": 2, "That": [2, 4], "give": 2, "chang": 2, "suggest": [2, 4], "chmod": 2, "x": [2, 4], "dockerfile_rn": 2, "10": 2, "docker": 3, "scientif": 4, "comput": 4, "perform": 4, "lawrenc": 4, "berkelei": 4, "nation": 4, "laboratori": 4, "spin": 4, "off": 4, "sylab": 4, "en": 4, "wikipedia": 4, "org": 4, "wiki": 4, "singularity_": 4, "strength": 4, "At": 4, "support": 4, "linux": 4, "simpl": 4, "user": 4, "mac": 4, "experiment": 4, "desktop": 4, "headach": 4, "hack": 4, "For": 4, "featur": 4, "root": 4, "account": 4, "sudo": 4, "easili": 4, "two": 4, "type": 4, "product": 4, "writabl": 4, "sandbox": 4, "trivia": 4, "nowadai": 4, "mai": 4, "sinc": 4, "apptain": 4, "fork": 4, "2021": 4, "so": 4, "far": 4, "most": 4, "codebas": 4, "eventu": 4, "could": 4, "former": 4, "alreadi": 4, "end": 4, "Of": 4, "life": 4, "its": 4, "continu": 4, "under": 4, "foundat": 4, "These": 4, "browser": 4, "discov": 4, "within": 4, "privat": 4, "r": 4, "build": 4, "sif": 4, "websit": 4, "gather": 4, "wa": 4, "prefer": 4, "9": 4, "pull": 4, "depot": 4, "galaxyproject": 4, "download": 4, "convers": 4, "best": 4, "those": 4, "biomed": 4, "field": 4, "link": 4, "onc": 4, "readi": 4, "straight": 4, "forward": 4, "exploratori": 4, "approach": 4, "equival": 4, "handi": 4, "move": 4, "around": 4, "notic": 4, "comparison": 4, "access": 4, "common": 4, "git": 4, "b7_input_s_chr19": 4, "By": 4, "inherit": 4, "profil": 4, "circumst": 4, "lead": 4, "unexpect": 4, "problem": 4, "own": 4, "clash": 4, "one": 4, "compar": 4, "modifi": 4, "samtool": 4, "consid": 4, "explor": 4, "fqidx": 4, "explicitli": 4, "3": 4, "6": 4, "home": 4, "sy": 4, "proc": 4, "var": 4, "resolv": 4, "passwd": 4, "ref": 4, "done": 4, "testout": 4, "b": 4, "testin": 4, "testdir": 4, "dummi": 4, "html": 4, "rm": 4, "cd": 4, "happen": 4, "c": 4, "evolv": 4, "don": 4, "worth": 4, "paramet": 4, "detail": 4, "doc": 4, "clean": 4, "preced": 4, "administr": 4}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"contain": [0, 1, 3, 4], "linux": 0, "what": [0, 1], "ar": 0, "virtual": 0, "machin": 0, "docker": [1, 2, 4], "introduct": [1, 4], "i": 1, "compon": 1, "imag": [1, 2, 4], "versu": 1, "podman": 1, "setup": 1, "vocabulari": 1, "us": 1, "exist": 1, "explor": 1, "hub": [1, 4], "pull": 1, "import": 1, "biocontain": [1, 4], "list": 1, "run": [1, 4], "e": 1, "start": 1, "p": 1, "check": 1, "statu": 1, "exec": [1, 4], "execut": [1, 4], "process": 1, "rm": 1, "rmi": 1, "clean": 1, "up": 1, "major": 1, "volum": [1, 4], "exercis": [1, 2, 4], "user": 1, "2": 2, "recip": 2, "build": 2, "your": 2, "own": 2, "o": 2, "command": 2, "updat": 2, "upgrad": 2, "packag": 2, "search": 2, "instal": 2, "basic": 2, "instruct": 2, "more": 2, "tag": 2, "scientif": 3, "crg": 3, "phd": 3, "cours": 3, "2023": 3, "singular": 4, "architectur": 4, "registri": 4, "via": 4, "quai": 4, "io": 4, "galaxi": 4, "project": 4, "prebuilt": 4, "shell": 4, "environ": 4, "control": 4, "advanc": 4, "aspect": 4, "bind": 4, "path": 4, "aka": 4, "tip": 4, "troubleshoot": 4, "fakeroot": 4, "cach": 4, "directori": 4, "global": 4, "configur": 4}, "envversion": {"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, "sphinx": 60}, "alltitles": {"Containers": [[0, "containers"]], "Linux containers": [[0, "linux-containers"]], "What are containers?": [[0, "what-are-containers"]], "Virtual machines or containers ?": [[0, "virtual-machines-or-containers"]], "Docker": [[1, "docker"]], "Introduction to Docker": [[1, "introduction-to-docker"]], "What is Docker?": [[1, "what-is-docker"]], "Docker components": [[1, "docker-components"]], "Images versus containers": [[1, "images-versus-containers"]], "Podman setup": [[1, "podman-setup"]], "Docker vocabulary": [[1, "docker-vocabulary"]], "Using existing images": [[1, "using-existing-images"]], "Explore Docker hub": [[1, "explore-docker-hub"]], "docker pull: import image": [[1, "docker-pull-import-image"]], "Biocontainers": [[1, "biocontainers"], [4, "biocontainers"]], "docker images: list images": [[1, "docker-images-list-images"]], "docker run: run image, i.e. start a container": [[1, "docker-run-run-image-i-e-start-a-container"]], "docker ps: check containers status": [[1, "docker-ps-check-containers-status"]], "docker exec: execute process in running container": [[1, "docker-exec-execute-process-in-running-container"]], "docker rm, docker rmi: clean up!": [[1, "docker-rm-docker-rmi-clean-up"]], "Major clean": [[1, "major-clean"]], "Volumes": [[1, "volumes"]], "Volume exercises": [[1, "volume-exercises"]], "docker run \u2013user": [[1, "docker-run-user"]], "Docker 2": [[2, "docker-2"]], "Docker recipes: build your own images": [[2, "docker-recipes-build-your-own-images"]], "OS commands in image building": [[2, "os-commands-in-image-building"]], "Update and upgrade packages": [[2, "update-and-upgrade-packages"]], "Search and install packages": [[2, "search-and-install-packages"]], "Building recipes": [[2, "building-recipes"]], "Basic instructions": [[2, "basic-instructions"]], "docker build": [[2, "docker-build"]], "More instructions": [[2, "more-instructions"]], "docker tag": [[2, "docker-tag"]], "Build exercise": [[2, "build-exercise"]], "Scientific Containers CRG PhD course 2023": [[3, "scientific-containers-crg-phd-course-2023"]], "Singularity": [[4, "singularity"]], "Introduction to Singularity": [[4, "introduction-to-singularity"]], "Singularity architecture": [[4, "singularity-architecture"]], "Container registries": [[4, "container-registries"]], "Docker Hub": [[4, "docker-hub"]], "Via quay.io": [[4, "via-quay-io"]], "Via Galaxy project prebuilt images": [[4, "via-galaxy-project-prebuilt-images"]], "Running and executing containers": [[4, "running-and-executing-containers"]], "Singularity shell": [[4, "singularity-shell"]], "Singularity exec": [[4, "singularity-exec"]], "Environment control": [[4, "environment-control"]], "Exercise": [[4, "exercise"], [4, "id1"]], "Singularity advanced aspects": [[4, "singularity-advanced-aspects"]], "Bind paths (aka volumes)": [[4, "bind-paths-aka-volumes"]], "Singularity tips": [[4, "singularity-tips"]], "Troubleshooting": [[4, "troubleshooting"]], "Fakeroot": [[4, "fakeroot"]], "Singularity cache directory": [[4, "singularity-cache-directory"]], "Global singularity configuration": [[4, "global-singularity-configuration"]]}, "indexentries": {}}) \ No newline at end of file +Search.setIndex({"docnames": ["containers", "docker", "docker_2", "index", "singularity"], "filenames": ["containers.rst", "docker.rst", "docker_2.rst", "index.rst", "singularity.rst"], "titles": ["Containers", "Docker", "Docker 2", "Scientific Containers CRG PhD course 2023", "Singularity"], "terms": {"A": [0, 1, 2], "can": [0, 1, 2, 4], "seen": 0, "minim": 0, "environ": [0, 1, 2], "us": [0, 2, 4], "ani": [0, 1], "compat": [0, 1], "beyond": 0, "i": [0, 2, 4], "time": [0, 4], "resourc": 0, "save": [0, 2], "thei": [0, 1, 4], "allow": 0, "control": 0, "softwar": [0, 1, 4], "instal": 0, "depend": [0, 2, 4], "reproduc": [0, 4], "analysi": 0, "u": [0, 1], "exactli": 0, "same": [0, 1, 2], "version": [0, 1, 2, 4], "tool": [0, 1, 4], "virtualis": 0, "containeris": 0, "aka": 0, "lightweight": 0, "abstract": 0, "physic": 0, "hardwar": 0, "applic": [0, 1], "layer": [0, 1, 2], "hypervisor": 0, "host": [0, 1, 2, 4], "kernel": 0, "o": 0, "do": [0, 1], "confus": [0, 4], "emul": 0, "bundl": 0, "all": [0, 1, 2, 4], "togeth": 0, "enabl": 0, "everi": [0, 2], "an": [0, 1, 2, 4], "oper": [0, 2], "system": [0, 1, 2, 4], "sourc": [0, 2, 4], "pro": [0, 1, 4], "con": 0, "adv": 0, "veri": 0, "similar": [0, 4], "full": 0, "high": [0, 1, 4], "divers": 0, "No": [0, 4], "need": [0, 4], "less": 0, "space": [0, 1], "better": 0, "portabl": [0, 4], "faster": 0, "than": 0, "easier": 0, "autom": 0, "distribut": 0, "recip": [0, 1], "more": [0, 1, 4], "slower": 0, "Not": 0, "good": [0, 2, 4], "some": [0, 1, 2, 4], "case": [0, 1, 2], "might": [0, 4], "still": 0, "even": [0, 2], "current": [0, 1, 2], "solut": [0, 2, 4], "platform": 1, "develop": [1, 4], "ship": 1, "infrastructur": 1, "code": 1, "first": [1, 2, 4], "2013": 1, "compani": 1, "origin": [1, 4], "dotcloud": 1, "2010": 1, "later": [1, 4], "name": [1, 2, 4], "establish": 1, "open": 1, "initi": [1, 4], "As": [1, 2], "commun": 1, "edit": [1, 4], "enterpris": 1, "There": 1, "increas": 1, "number": [1, 2], "altern": 1, "technologi": 1, "provid": [1, 4], "mani": 1, "them": [1, 4], "ar": [1, 2, 4], "base": [1, 2], "from": [1, 2, 4], "stack": 1, "usual": 1, "try": [1, 2], "address": 1, "specif": [1, 2], "weak": [1, 4], "point": [1, 4], "exampl": [1, 2, 4], "singular": [1, 3], "which": [1, 2, 4], "we": [1, 2, 4], "introduc": 1, "thi": [1, 2, 4], "cours": 1, "focus": [1, 4], "hpc": [1, 4], "anoth": [1, 2], "http": [1, 2, 4], "io": [1, 2], "__": 1, "keep": 1, "function": [1, 4], "differ": [1, 2, 4], "focu": [1, 4], "daemon": [1, 4], "permiss": [1, 4], "command": [1, 4], "alia": 1, "our": 1, "read": [1, 4], "onli": [1, 2, 4], "templat": 1, "have": [1, 2, 4], "sever": 1, "set": [1, 2], "inert": 1, "instanc": [1, 2, 4], "call": [1, 2], "when": [1, 2, 4], "you": [1, 2, 4], "The": [1, 2, 4], "cake": 1, "make": [1, 2], "like": 1, "given": [1, 2], "stackoverflow": 1, "com": [1, 2, 4], "question": [1, 2], "23735149": 1, "between": [1, 2], "place": [1, 4], "follow": [1, 2], "bit": 1, "config": 1, "storag": 1, "conf": [1, 4], "driver": 1, "overlai": 1, "graphroot": 1, "tmp": [1, 4], "local": [1, 2, 4], "share": [1, 4], "option": [1, 2, 4], "mount_program": 1, "usr": [1, 2, 4], "bin": [1, 2, 4], "fuse": 1, "overlayf": 1, "get": [1, 2], "help": [1, 4], "store": [1, 4], "registri": 1, "main": [1, 4], "public": [1, 4], "let": [1, 2, 4], "": [1, 2, 4], "search": 1, "keyword": 1, "ubuntu": [1, 2], "latest": [1, 2], "releas": 1, "choos": 1, "fetch": 1, "tag": 1, "22": 1, "04": [1, 2], "directori": [1, 2], "bioinformat": [1, 4], "relat": 1, "entri": 1, "quai": 1, "redhat": 1, "normal": [1, 4], "creat": [1, 4], "bioconda": [1, 2], "fastqc": [1, 4], "v0": [1, 4], "11": [1, 4], "9_cv7": [1, 4], "each": [1, 2], "ha": 1, "uniqu": 1, "id": [1, 2], "now": [1, 4], "want": 1, "insid": [1, 2, 4], "fresh": 1, "activ": 1, "static": 1, "format": 1, "l": [1, 4], "your": [1, 4], "work": [1, 2, 4], "result": [1, 2], "program": [1, 2, 4], "whoami": 1, "cat": 1, "etc": [1, 2, 4], "issu": [1, 4], "either": 1, "line": [1, 2, 4], "see": [1, 2], "abov": 1, "interact": 1, "enter": 1, "bash": [1, 2, 4], "background": 1, "detach": 1, "tail": 1, "f": [1, 2, 4], "dev": [1, 2], "null": 1, "myubuntu": 1, "whether": 1, "unam": 1, "df": 1, "remov": [1, 4], "unus": 1, "other": [1, 4], "WITH": 1, "care": 1, "prune": 1, "non": 1, "much": 1, "refer": 1, "www": 1, "digitalocean": 1, "tutori": [1, 2], "how": [1, 4], "fulli": 1, "isol": [1, 4], "It": [1, 2, 4], "necessari": 1, "mount": [1, 4], "order": [1, 2], "handl": 1, "input": 1, "output": [1, 2], "file": [1, 2, 4], "syntax": [1, 2, 4], "v": 1, "mkdir": [1, 2, 4], "test": [1, 4], "touch": [1, 4], "pwd": [1, 4], "scratch": [1, 4], "fastqc_contain": 1, "ti": [1, 4], "exit": [1, 4], "copi": [1, 2, 4], "2": [1, 3, 4], "fastq": [1, 4], "avail": [1, 2, 4], "dataset": 1, "github": [1, 3], "repositori": [1, 2, 3, 4], "gz": [1, 4], "outsid": [1, 4], "possibl": 1, "append": 1, "conveni": [1, 4], "would": [1, 2, 4], "g": [1, 2, 4], "user_test": 1, "userfil": 1, "underli": 2, "wai": [2, 4], "know": 2, "popular": [2, 4], "ones": [2, 4], "debian": 2, "cento": 2, "alpin": 2, "conda": 2, "anaconda": 2, "forg": 2, "In": 2, "apt": 2, "y": 2, "yum": 2, "check": [2, 4], "libxml2": 2, "devel": 2, "x86_64": 2, "note": [2, 4], "br": 2, "import": 2, "context": 2, "mean": 2, "answer": 2, "ye": 2, "regard": 2, "should": 2, "text": 2, "default": [2, 4], "dockerfil": 2, "row": 2, "correspond": 2, "final": 2, "parent": 2, "typic": 2, "18": 2, "run": 2, "execut": 2, "filesystem": [2, 4], "think": 2, "about": 2, "essenti": 2, "what": [2, 4], "freshli": 2, "wget": 2, "implicit": 2, "look": 2, "stand": 2, "process": [2, 4], "sens": 2, "avoid": [2, 4], "overpopul": 2, "actual": 2, "defin": 2, "dure": 2, "t": [2, 4], "imagenam": 2, "If": [2, 4], "mytestimag": 2, "over": 2, "popul": 2, "inspect": 2, "includ": 2, "e": [2, 4], "dockerignor": 2, "specifi": 2, "path": 2, "inform": [2, 4], "codefresh": 2, "ignor": 2, "last": [2, 4], "successfulli": 2, "built": 2, "go": 2, "newli": 2, "list": 2, "Then": 2, "f9f41698e2f8": 2, "workdir": 2, "subsequ": 2, "action": 2, "add": 2, "explain": 2, "here": [2, 4], "machin": 2, "also": [2, 4], "url": 2, "tar": 2, "archiv": 2, "automat": 2, "extract": 2, "upon": 2, "being": 2, "sai": 2, "jpg": 2, "destin": 2, "sophist": 2, "p": 2, "data": [2, 4], "env": [2, 4], "arg": 2, "variabl": [2, 4], "valu": 2, "while": 2, "futur": 2, "contain": 2, "cmd": 2, "entrypoint": 2, "gener": [2, 4], "start": 2, "alwai": 2, "argument": 2, "fed": 2, "below": 2, "without": [2, 4], "echo": 2, "hello": 2, "world": [2, 4], "moon": 2, "complex": 2, "maintain": 2, "toni": 2, "hermoso": 2, "pulido": 2, "crg": 2, "eu": 2, "cdn": 2, "wp": 2, "nginx": 2, "content": [2, 3, 4], "upload": 2, "2016": [2, 4], "07": 2, "swarm": 2, "hero2": 2, "png": 2, "1": [2, 4], "medium": 2, "max": 2, "1600": 2, "_nqn6_ynxs29m8vfzwyleg": 2, "To": 2, "e23aaea5dff1": 2, "ubuntu_wget": 2, "0": [2, 4], "random": 2, "short": 2, "script": 2, "random_numb": 2, "seq": 2, "1000": 2, "shuf": 2, "head": 2, "interg": 2, "integ": 2, "select": 2, "write": [2, 4], "7": 2, "That": [2, 4], "give": 2, "chang": 2, "suggest": [2, 4], "chmod": 2, "x": [2, 4], "dockerfile_rn": 2, "10": 2, "docker": 3, "scientif": 4, "comput": 4, "perform": 4, "lawrenc": 4, "berkelei": 4, "nation": 4, "laboratori": 4, "spin": 4, "off": 4, "sylab": 4, "en": 4, "wikipedia": 4, "org": 4, "wiki": 4, "singularity_": 4, "strength": 4, "At": 4, "support": 4, "linux": 4, "simpl": 4, "user": 4, "mac": 4, "experiment": 4, "desktop": 4, "headach": 4, "hack": 4, "For": 4, "featur": 4, "root": 4, "account": 4, "sudo": 4, "easili": 4, "two": 4, "type": 4, "product": 4, "writabl": 4, "sandbox": 4, "trivia": 4, "nowadai": 4, "mai": 4, "sinc": 4, "apptain": 4, "fork": 4, "2021": 4, "so": 4, "far": 4, "most": 4, "codebas": 4, "eventu": 4, "could": 4, "former": 4, "alreadi": 4, "end": 4, "Of": 4, "life": 4, "its": 4, "continu": 4, "under": 4, "foundat": 4, "These": 4, "browser": 4, "discov": 4, "within": 4, "privat": 4, "r": 4, "build": 4, "sif": 4, "websit": 4, "gather": 4, "wa": 4, "prefer": 4, "9": 4, "pull": 4, "depot": 4, "galaxyproject": 4, "download": 4, "convers": 4, "best": 4, "those": 4, "biomed": 4, "field": 4, "link": 4, "onc": 4, "readi": 4, "straight": 4, "forward": 4, "exploratori": 4, "approach": 4, "equival": 4, "handi": 4, "move": 4, "around": 4, "notic": 4, "comparison": 4, "access": 4, "common": 4, "git": 4, "b7_input_s_chr19": 4, "By": 4, "inherit": 4, "profil": 4, "circumst": 4, "lead": 4, "unexpect": 4, "problem": 4, "own": 4, "clash": 4, "one": 4, "compar": 4, "modifi": 4, "samtool": 4, "consid": 4, "explor": 4, "fqidx": 4, "explicitli": 4, "3": 4, "6": 4, "home": 4, "sy": 4, "proc": 4, "var": 4, "resolv": 4, "passwd": 4, "ref": 4, "done": 4, "testout": 4, "b": 4, "testin": 4, "testdir": 4, "dummi": 4, "html": 4, "rm": 4, "cd": 4, "happen": 4, "c": 4, "evolv": 4, "don": 4, "worth": 4, "paramet": 4, "detail": 4, "doc": 4, "clean": 4, "preced": 4, "administr": 4}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"contain": [0, 1, 3, 4], "linux": 0, "what": [0, 1], "ar": 0, "virtual": 0, "machin": 0, "docker": [1, 2, 4], "introduct": [1, 4], "i": 1, "compon": 1, "imag": [1, 2, 4], "versu": 1, "podman": 1, "setup": 1, "vocabulari": 1, "us": 1, "exist": 1, "explor": 1, "hub": [1, 4], "pull": 1, "import": 1, "biocontain": [1, 4], "list": 1, "run": [1, 4], "e": 1, "start": 1, "p": 1, "check": 1, "statu": 1, "exec": [1, 4], "execut": [1, 4], "process": 1, "rm": 1, "rmi": 1, "clean": 1, "up": 1, "major": 1, "volum": [1, 4], "exercis": [1, 2, 4], "user": 1, "2": 2, "recip": 2, "build": 2, "your": 2, "own": 2, "o": 2, "command": 2, "updat": 2, "upgrad": 2, "packag": 2, "search": 2, "instal": 2, "basic": 2, "instruct": 2, "more": 2, "tag": 2, "scientif": 3, "crg": 3, "phd": 3, "cours": 3, "2023": 3, "singular": 4, "architectur": 4, "registri": 4, "via": 4, "quai": 4, "io": 4, "galaxi": 4, "project": 4, "prebuilt": 4, "shell": 4, "environ": 4, "control": 4, "advanc": 4, "aspect": 4, "bind": 4, "path": 4, "aka": 4, "tip": 4, "troubleshoot": 4, "fakeroot": 4, "cach": 4, "directori": 4, "global": 4, "configur": 4}, "envversion": {"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, "sphinx": 60}, "alltitles": {"Containers": [[0, "containers"]], "Linux containers": [[0, "linux-containers"]], "What are containers?": [[0, "what-are-containers"]], "Virtual machines or containers ?": [[0, "virtual-machines-or-containers"]], "Docker": [[1, "docker"]], "Introduction to Docker": [[1, "introduction-to-docker"]], "What is Docker?": [[1, "what-is-docker"]], "Docker components": [[1, "docker-components"]], "Images versus containers": [[1, "images-versus-containers"]], "Podman setup": [[1, "podman-setup"]], "Docker vocabulary": [[1, "docker-vocabulary"]], "Using existing images": [[1, "using-existing-images"]], "Explore Docker hub": [[1, "explore-docker-hub"]], "docker pull: import image": [[1, "docker-pull-import-image"]], "Biocontainers": [[1, "biocontainers"], [4, "biocontainers"]], "docker images: list images": [[1, "docker-images-list-images"]], "docker run: run image, i.e. start a container": [[1, "docker-run-run-image-i-e-start-a-container"]], "docker ps: check containers status": [[1, "docker-ps-check-containers-status"]], "docker exec: execute process in running container": [[1, "docker-exec-execute-process-in-running-container"]], "docker rm, docker rmi: clean up!": [[1, "docker-rm-docker-rmi-clean-up"]], "Major clean": [[1, "major-clean"]], "Volumes": [[1, "volumes"]], "Volume exercises": [[1, "volume-exercises"]], "docker run \u2013user": [[1, "docker-run-user"]], "Docker 2": [[2, "docker-2"]], "Docker recipes: build your own images": [[2, "docker-recipes-build-your-own-images"]], "OS commands in image building": [[2, "os-commands-in-image-building"]], "Update and upgrade packages": [[2, "update-and-upgrade-packages"]], "Search and install packages": [[2, "search-and-install-packages"]], "Building recipes": [[2, "building-recipes"]], "Basic instructions": [[2, "basic-instructions"]], "docker build": [[2, "docker-build"]], "More instructions": [[2, "more-instructions"]], "docker tag": [[2, "docker-tag"]], "Build exercise": [[2, "build-exercise"]], "Scientific Containers CRG PhD course 2023": [[3, "scientific-containers-crg-phd-course-2023"]], "Singularity": [[4, "singularity"]], "Introduction to Singularity": [[4, "introduction-to-singularity"]], "Singularity architecture": [[4, "singularity-architecture"]], "Container registries": [[4, "container-registries"]], "Docker Hub": [[4, "docker-hub"]], "Via quay.io": [[4, "via-quay-io"]], "Via Galaxy project prebuilt images": [[4, "via-galaxy-project-prebuilt-images"]], "Running and executing containers": [[4, "running-and-executing-containers"]], "Singularity shell": [[4, "singularity-shell"]], "Singularity exec": [[4, "singularity-exec"]], "Environment control": [[4, "environment-control"]], "Exercise": [[4, "exercise"], [4, "id1"]], "Singularity advanced aspects": [[4, "singularity-advanced-aspects"]], "Bind paths (aka volumes)": [[4, "bind-paths-aka-volumes"]], "Singularity tips": [[4, "singularity-tips"]], "Troubleshooting": [[4, "troubleshooting"]], "Fakeroot": [[4, "fakeroot"]], "Singularity cache directory": [[4, "singularity-cache-directory"]], "Global singularity configuration": [[4, "global-singularity-configuration"]]}, "indexentries": {}}) \ No newline at end of file