Index

Symbols

1-001

2-003 3-001

A

absolute path access WSL2 symlinked files on Windows add changes to previous commit with DataLad add container image to dataset with DataLad addurls DataLad command adjusted branch git-annex concept in adjusted mode unlocked files

adjusted mode git-annex concept, [1] on Windows amend commit message with Git annex git-annex concept annex key git-annex concept annex UUID annex uuid git-annex concept

B

bare Git repositories bare repository Git concept bash Bitbucket dataset hosting

branch Git concept, [1] broken symlink build container image with Singularity

C

cat-file Git command CentOS see also 'on Redhat/Fedora' change historical commit messages with Git change the last commit message with DataLad check dataset for modification with DataLad, [1], [2] check out particular version with Git, [1] checkout Git command, [1] checksum see also 'shasum' clone DataLad command, [1], [2], [3], [4], [5], [6], [7], [8] DataLad concept, [1] Git concept clone (ephemeral) DataLad concept clone dataset with DataLad clone dataset (set location description) with DataLad clone into another dataset with DataLad command Line command line concept globbing pager tab completion commit Git concept commit message Git concept recommendation common data source DataLad concept compute checksum in a terminal compute node concepts SSH SSH key, [1] Conda see also 'with Conda' conda config Git command configuration DataLad command configuration file .datalad/config .git/config .gitattributes .gitmodules Git concept configuration item datalad.dataset.id, [1] datalad.extensions.load datalad.get.subdataset-source-candidate-<name> datalad.gitlab-<name>-project datalad.gitlab-default-pathseparator datalad.gitlab-default-projectname datalad.locations.dataset-procedures datalad.locations.system-procedures datalad.locations.user-procedures datalad.log.level, [1] datalad.procedures.<name>.call-format datalad.procedures.<name>.help datalad.result-hook.<name>.call-json datalad.result-hook.<name>.match-json remote.<name>.annex-ignore

configuration.item datalad.containers.<name>.cmdexec configure default editor with Git configure editor with Git configure sibling with DataLad configure user identity with Git configure verbosity of command output with DataLad configure which branches to push with Git container software container concept container concept container image recipe container image container image registration DataLad concept container recipe containers-add DataLad command containers-list DataLad command containers-remove DataLad command containers-run DataLad command content pointer file git-annex concept, [1] copy file to other dataset with DataLad copy-file DataLad command copyright corresponding branch in adjusted mode, [1], [2], [3], [4], [5] create DataLad command create and publish dataset as dependency with DataLad create dataset DataLad concept with DataLad, [1] create heredoc in a terminal create sibling with DataLad create-sibling DataLad command, [1], [2] create-sibling-gin DataLad command create-sibling-github DataLad command, [1], [2], [3] create-sibling-gitlab DataLad command, [1] create-sibling-ria DataLad command, [1], [2], [3] credential entry GitHub token storage crippled file system git-annex concept curl instead of wget on Windows

D

DataLad see also 'with DataLad' DataLad command addurls clone, [1], [2], [3], [4], [5], [6], [7], [8] configuration containers-add containers-list containers-remove containers-run copy-file create create-sibling, [1], [2] create-sibling-gin create-sibling-github, [1], [2], [3] create-sibling-gitlab, [1] create-sibling-ria, [1], [2], [3] diff, [1], [2], [3] drop, [1], [2] get push remove rerun run, [1] run-procedure save, [1] save --amend siblings status, [1] subdatasets, [1] unlock update wtf DataLad concept clone, [1] common data source container image registration create dataset dataset dataset identifier dataset nesting extension get log level, [1] publication dependency, [1] push, [1], [2], [3] Remote Indexed Archive result hooks RIA store run procedure run record sibling sibling (GitHub) subdataset superdataset update DataLad dataset DataLad extension, [1] DataLad Gooey DataLad subdataset DataLad superdataset

dataset DataLad concept dataset configuration dataset content organization recommendation dataset hosting Bitbucket GIN, [1] GitHub, [1], [2] GitLab, [1] RIA dataset ID dataset identifier DataLad concept dataset nesting DataLad concept with DataLad dataset procedure apply more than one configuration apply to subdatasets discover run run on dataset creation text2git datasets procedures write your own Debian see also 'on Debian/Ubuntu' debugging, [1] declare command input with DataLad run declare command output with DataLad run determine version with Python diff DataLad command, [1], [2], [3] Git command, [1] discover dataset procedure discover dataset procedures with DataLad display directory tree on Windows Docker hub, [1], [2] installation Docker-Hub DOI download file with curl with wget drop DataLad command, [1], [2] drop (LFS) with DataLad drop file content with DataLad dropunused git-annex command, [1] dry-run with DataLad run

E

elevated storage demand in adjusted mode environment variable, [1] ephemeral clone exit pager in a terminal

explicit input/output declaration with DataLad run extension DataLad concept extractor

F

Fedora see also 'on Redhat/Fedora' file content identifier git-annex concept file system concept path (absolute) path (relative) permissions symlink

files are unlocked by default on Windows, [1], [2] filter history with Git fix git-annex command force-push fork Git concept

G

get DataLad command DataLad concept get all dataset content with DataLad get file content with DataLad get help with Git get system information with DataLad GIN Git Git command cat-file checkout, [1] config diff, [1] gitk log, [1], [2], [3], [4], [5], [6] rebase revert show Git concept bare repository branch, [1] clone commit commit message fork HEAD main branch master branch merge merge request pull request push (forced) ref remote squash submodule tag, [1]

Git config file git-annex see also 'with git-annex' git-annex branch git-annex concept git-annex command dropunused, [1] fix unused, [1] whereis git-annex concept adjusted branch adjusted mode, [1] annex annex key annex uuid content pointer file, [1] crippled file system file content identifier git-annex branch key location identifier special remote GitHub dataset hosting GitHub token credential gitk Git command GitLab dataset hosting globbing

H

HEAD Git concept here-document see 'heredoc' heredoc, [1] on Windows in a terminal hidden file name extensions on Windows high-performance computing see 'HPC'

high-throughput computing see 'HTC' HPC see also 'on HPC' HTC http https hub Docker, [1], [2] Human Connectome Project (HCP)

I

image software container concept in a terminal compute checksum create heredoc exit pager show file size update heredoc use command options in adjusted mode adjusted branch corresponding branch, [1], [2], [3], [4], [5] elevated storage demand unlocked files, [1] install 7-zip on Windows install DataLad on Debian/Ubuntu on HPC on Mac on Redhat/Fedora on Windows on WSL2 with Conda with pip

install Docker on Windows install Git on Windows install git-annex on Windows install ImageMagick on Windows install Python on Windows installation 7-Zip DataLad Docker Git git-annex ImageMagick Python

K

key git-annex concept

L

licenses line continuation on Windows in a terminal list dataset siblings with DataLad list known containers with DataLad list subdatasets with DataLad

location identifier git-annex concept log Git command, [1], [2], [3], [4], [5], [6] log level DataLad concept, [1] logging

M

Mac see also 'on Mac' main main branch Git concept Make Makefile manpage master master branch Git concept merge Git concept

merge request Git concept metadata metadata extractor DataLad concept modify configuration with Git move file to other dataset with DataLad move subdataset with Git multiple command inputs with DataLad run

N

nano terminal command no staging with DataLad

no symlinks on Windows, [1]

O

object tree git-annex concept object-tree OHBM 2020 Poster on Debian/Ubuntu install DataLad on HPC install DataLad on Mac install DataLad placeholder files on Redhat/Fedora install DataLad on Unix-like systems terminal commands on Windows access WSL2 symlinked files adjusted mode curl instead of wget display directory tree files are unlocked by default, [1], [2] hidden file name extensions install 7-zip install DataLad install Docker install Git install git-annex install ImageMagick install Python no symlinks, [1] python instead of python3 show history terminal commands typed credentials are not displayed

on Windows in a terminal heredoc line continuation on Windows with DataLad show dataset modification show dataset modification for particular path on Windows with Git show dataset modification show history for particular paths on WSL2 install DataLad Open Science Framework operating system concept environment variable, [1] pipe stderr stdin stdout OSF

P

pager path globbing with DataLad run, [1] paths permissions pip see also 'with pip' terminal command pipe placeholder files on Mac procedures protocol http https provenance publication dependency DataLad concept, [1]

pull request Git concept push DataLad command DataLad concept, [1], [2], [3] push (dataset) with DataLad push (forced) Git concept push (tag) with DataLad with Git Python see also 'with Python' python instead of python3 on Windows

R

rebase Git command recipe software container concept recommendation commit message dataset content organization RedHat see also 'on Redhat/Fedora' ref Git concept register file with URL in dataset with DataLad register sibling in dataset with DataLad relative path remote Git concept Remote Indexed Archive DataLad concept Remote Indexed Archive (RIA) store, [1] remove DataLad command remove dataset sibling with DataLad remove sensitive information with Git rename file with DataLad with Git reproducible paper with DataLad rerun DataLad command rerun command with DataLad, [1] resolve merge conflict with Git

result hooks DataLad concept revert Git command revert multiple commit with Git rewrite history with Git RIA dataset hosting RIA store DataLad concept run DataLad command, [1] dataset procedure run command with DataLad containers-run run command on dirty dataset with DataLad run run command with curly brackets with DataLad run run command with provenance capture with DataLad, [1], [2] with DataLad run, [1] run dataset procedure with DataLad run dataset procedure on dataset creation with DataLad run on dataset creation dataset procedure run procedure DataLad concept run record DataLad concept run-procedure DataLad command run-procedures

S

save DataLad command, [1] save --amend DataLad command save already tracked files only with DataLad save dataset modification with DataLad, [1], [2] save file content directly in Git (no annex) with DataLad save modification in nested dataset with DataLad sed terminal command set configuration with DataLad set description for dataset location with DataLad, [1] shasum shebang shell, [1] bash zsh shell commands see 'terminal commands' show Git command show commit patches with Git show dataset modification on Windows with DataLad on Windows with Git with DataLad with Git show dataset modification for particular path on Windows with DataLad show dataset size with DataLad show file content availability with git-annex show file size in a terminal show history on Windows with Git show history (compact) with Git

show history (reverse) with Git show history for particular paths on Windows with Git with Git show last commit with Git sibling DataLad concept sibling (GitHub) DataLad concept siblings DataLad command Singularity Singularity-Hub software container software container concept container image recipe special remote git-annex concept squash Git concept SSH key, [1] server SSH key SSH server status DataLad command, [1] stderr stdin stdout stop content tracking with Git with git-annex subdataset DataLad concept subdatasets DataLad command, [1] submodule Git concept superdataset DataLad concept symlink broken

T

tab completion, [1] tag Git concept, [1] tag dataset version with DataLad temporary working directory change with Git terminal, [1] see also 'in a terminal' terminal command nano pip sed tig tree, [1], [2] vim

terminal commands on Unix-like systems on Windows the DataLad superdataset /// tig terminal command tree terminal command, [1], [2] typed credentials are not displayed on Windows

U

Ubuntu see also 'on Debian/Ubuntu' unlock DataLad command unlock file with DataLad unlocked files in adjusted mode, [1] unset configuration with Git unused git-annex command, [1] update DataLad command DataLad concept update dataset from particular sibling with DataLad update dataset with remote change with DataLad update heredoc in a terminal

use command options in a terminal use DataLad API with Matlab with Python with R Usecase Basic provenance tracking Basic Reproducible Neuroimaging Collaboration Encrypted data storage and transport Machine Learning Analysis Remote Indexed Archive (RIA) store Reproducible Neuroimaging reproducible paper Scaling up: 80TB and 15 million files Student supervision Using Globus as data store UUID

V

version control vim terminal command

virtual environment

W

whereis git-annex command Windows see also 'on Windows' with Conda install DataLad with curl download file with DataLad add changes to previous commit add container image to dataset change the last commit message check dataset for modification, [1], [2] clone dataset clone dataset (set location description) clone into another dataset configure sibling configure verbosity of command output copy file to other dataset create and publish dataset as dependency create dataset, [1] create sibling dataset nesting discover dataset procedures drop (LFS) drop file content get all dataset content get file content get system information list dataset siblings list known containers list subdatasets move file to other dataset no staging push (dataset) push (tag) register file with URL in dataset register sibling in dataset remove dataset sibling rename file reproducible paper rerun command, [1] run command with provenance capture, [1], [2] run dataset procedure run dataset procedure on dataset creation save already tracked files only save dataset modification, [1], [2] save file content directly in Git (no annex) save modification in nested dataset set configuration set description for dataset location, [1] show dataset modification show dataset size tag dataset version unlock file update dataset from particular sibling update dataset with remote change work on published YODA dataset with DataLad containers-run run command

with DataLad run declare command input declare command output dry-run explicit input/output declaration multiple command inputs path globbing, [1] run command on dirty dataset run command with curly brackets run command with provenance capture, [1] with Git amend commit message change historical commit messages check out particular version, [1] configure default editor configure editor configure which branches to push filter history get help modify configuration move subdataset push (tag) remove sensitive information rename file resolve merge conflict revert multiple commit rewrite history show commit patches show dataset modification show history show history (compact) show history (reverse) show history for particular paths show last commit stop content tracking temporary working directory change unset configuration with git-annex show file content availability stop content tracking with Matlab use DataLad API with pip install DataLad with Python determine version use DataLad API with R use DataLad API with Singularity build container image with wget download file work on published YODA dataset with DataLad WSL WSL2 see also 'on WSL2' symlink access wtf DataLad command

Y

YODA principles

Z

zsh