git-annex/doc/git-annex.mdwn

# NAME

git-annex - manage files with git, without checking their contents in

# SYNOPSIS

git annex command [params ...]

# DESCRIPTION

git-annex allows managing files with git, without checking the file
contents into git. While that may seem paradoxical, it is useful when
dealing with files larger than git can currently easily handle, whether due
to limitations in memory, checksumming time, or disk space.

Even without file content tracking, being able to manage files with git,
move files around and delete files with versioned directory trees, and use
branches and distributed clones, are all very handy reasons to use git. And
annexed files can co-exist in the same git repository with regularly
versioned files, which is convenient for maintaining documents, Makefiles,
etc that are associated with annexed files but that benefit from full
revision control.

When a file is annexed, its content is moved into a key-value store, and
a symlink is made that points to the content. These symlinks are checked into
git and versioned like regular files. You can move them around, delete 
them, and so on. Pushing to another git repository will make git-annex
there aware of the annexed file, and it can be used to retrieve its
content from the key-value store.

# EXAMPLES

	# git annex get video/hackity_hack_and_kaxxt.mov
	get video/_why_hackity_hack_and_kaxxt.mov (not available)
	  I was unable to access these remotes: server
	  Try making some of these repositories available:
	  	5863d8c0-d9a9-11df-adb2-af51e6559a49  -- my home file server
	   	58d84e8a-d9ae-11df-a1aa-ab9aa8c00826  -- portable USB drive
	   	ca20064c-dbb5-11df-b2fe-002170d25c55  -- backup SATA drive
	failed
	# sudo mount /media/usb
	# git remote add usbdrive /media/usb
	# git annex get video/hackity_hack_and_kaxxt.mov
	get video/hackity_hack_and_kaxxt.mov (from usbdrive...) ok
	
	# git annex add iso
	add iso/Debian_5.0.iso ok
	
	# git annex drop iso/Debian_4.0.iso
	drop iso/Debian_4.0.iso ok
	
	# git annex move iso --to=usbdrive
	move iso/Debian_5.0.iso (moving to usbdrive...) ok

# COMMONLY USED COMMANDS

Like many git commands, git-annex can be passed a path that 
is either a file or a directory. In the latter case it acts on all relevant
files in the directory. When no path is specified, most git-annex commands
default to acting on all relevant files in the current directory (and
subdirectories).

* add [path ...]

  Adds files in the path to the annex. Files that are already checked into
  git, or that git has been configured to ignore will be silently skipped.
  (Use --force to add ignored files.) Dotfiles are skipped unless explicitly
  listed.

* get [path ...]

  Makes the content of annexed files available in this repository. This
  will involve copying them from another repository, or downloading them,
  or transferring them from some kind of key-value store.

  Normally git-annex will choose which repository to copy the content from,
  but you can override this using the --from option.

* drop [path ...]

  Drops the content of annexed files from this repository. 

  git-annex will refuse to drop content if it cannot verify it is
  safe to do so. This can be overridden with the --force switch.

  To drop content from a remote, specify --from.

* move [path ...]
  
  When used with the --from option, moves the content of annexed files
  from the specified repository to the current one.

  When used with the --to option, moves the content of annexed files from
  the current repository to the specified one.

* copy [path ...]

  When used with the --from option, copies the content of annexed files
  from the specified repository to the current one.

  When used with the --to option, copies the content of annexed files from
  the current repository to the specified one.

  To avoid contacting the remote to check if it has every file, specify --fast

* unlock [path ...]

  Normally, the content of annexed files is protected from being changed.
  Unlocking a annexed file allows it to be modified. This replaces the
  symlink for each specified file with a copy of the file's content.
  You can then modify it and `git annex add` (or `git commit`) to inject
  it back into the annex.

* edit [path ...]

  This is an alias for the unlock command. May be easier to remember,
  if you think of this as allowing you to edit an annexed file.

* lock [path ...]

  Use this to undo an unlock command if you don't want to modify
  the files, or have made modifications you want to discard.

* sync [remote ...]

  Use this command when you want to synchronize the local repository with
  one or more of its remotes. You can specifiy the remotes to sync with;
  the default is to sync with all remotes. Or specify --fast to sync with
  the remotes with the lowest annex-cost value.

  The sync process involves first committing all local changes (git commit -a),
  then fetching and merging the `synced/master` and the `git-annex` branch
  from the remote repositories and finally pushing the changes back to
  those branches on the remote repositories. You can use standard git
  commands to do each of those steps by hand, or if you don't want to
  worry about the details, you can use sync.

  Note that syncing with a remote will not update the remote's working
  tree with changes made to the local repository. However, those changes
  are pushed to the remote, so can be merged into its working tree
  by running "git annex sync" on the remote.

  Note that sync does not transfer any file contents from or to the remote
  repositories.

* addurl [url ...]

  Downloads each url to its own file, which is added to the annex.

  To avoid immediately downloading the url, specify --fast.

  Normally the filename is based on the full url, so will look like
  "www.example.com_dir_subdir_bigfile". For a shorter filename, specify
  --pathdepth=N. For example, --pathdepth=1 will use "dir/subdir/bigfile",
  while --pathdepth=3 will use "bigfile". It can also be negative;
  --pathdepth=-2 will use the last two parts of the url.

  Or, to directly specify what file the url is added to, specify --file.
  This changes the behavior; now all the specified urls are recorded as
  alternate locations from which the file can be downloaded. In this mode,
  addurl can be used both to add new files, or to add urls to existing files.

# REPOSITORY SETUP COMMANDS

* init [description]

  Until a repository (or one of its remotes) has been initialized,
  git-annex will refuse to operate on it, to avoid accidentially
  using it in a repository that was not intended to have an annex.

  It's useful, but not mandatory, to initialize each new clone
  of a repository with its own description.

* describe repository description

  Changes the description of a repository.

  The repository to describe can be specified by git remote name or
  by uuid. To change the description of the current repository, use
  "here".

* initremote name [param=value ...]

  Sets up a special remote. The remote's
  configuration is specified by the parameters. If a remote
  with the specified name has already been configured, its configuration
  is modified by any values specified. In either case, the remote will be
  added to `.git/config`.

  Example Amazon S3 remote:

	initremote mys3 type=S3 encryption=none datacenter=EU

* trust [repository ...]

  Records that a repository is trusted to not unexpectedly lose
  content. Use with care.

  To trust the current repository, use "here".

* untrust [repository ...]

  Records that a repository is not trusted and could lose content
  at any time.

* semitrust [repository ...]

  Returns a repository to the default semi trusted state.

* dead [repository ...]

  Indicates that the repository has been irretrevably lost.
  (To undo, use semitrust.)

# REPOSITORY MAINTENANCE COMMANDS

* fsck [path ...]

  With no parameters, this command checks the whole annex for consistency,
  and warns about or fixes any problems found.

  With parameters, only the specified files are checked.

  To check a remote to fsck, specify --from.
  
  To avoid expensive checksum calculations (and expensive transfers when
  fscking a remote), specify --fast

* unused

  Checks the annex for data that does not correspond to any files present
  in any tag or branch, and prints a numbered list of the data.

  To only show unused temp and bad files, specify --fast.

  To check for annexed data on a remote, specify --from.

* dropunused [number ...]

  Drops the data corresponding to the numbers, as listed by the last
  `git annex unused`

  To drop the data from a remote, specify --from.

* merge

  Automatically merges remote tracking branches */git-annex into
  the git-annex branch. While git-annex mostly handles keeping the
  git-annex branch merged automatically, if you find you are unable
  to push the git-annex branch due non-fast-forward, this will fix it.

* fix [path ...]

  Fixes up symlinks that have become broken to again point to annexed content.
  This is useful to run if you have been moving the symlinks around,
  but is done automatically when committing a change with git too.

* upgrade

  Upgrades the repository to current layout.

# QUERY COMMANDS

* version

  Shows the version of git-annex, as well as repository version information.

* find [path ...]

  Outputs a list of annexed files in the specified path. With no path,
  finds files in the current directory and its subdirectories.

  By default, only lists annexed files whose content is currently present.
  This can be changed by specifying file matching options. To list all
  annexed files, present or not, specify --include "*". To list all
  annexed files whose content is not present, specify --not --in=here

  To output filenames terminated with nulls, for use with xargs -0,
  specify --print0. Or, a custom output formatting can be specified using
  --format. The default output format is the same as --format='${file}\\n'

  These variables are available for use in formats: file, key, backend,
  bytesize, humansize

* whereis [path ...]

  Displays a list of repositories known to contain the content of the
  specified file or files.

* log [path ...]

  Displays the location log for the specified file or files,
  showing each repository they were added to ("+") and removed from ("-").

  To limit how far back to seach for location log changes, the options
  --since, --after, --until, --before, and --max-count can be specified.
  They are passed through to git log. For example, --since "1 month ago"

  To generate output suitable for the gource visualisation program,
  specify --gource.

* status

  Displays some statistics and other information, including how much data
  is in the annex and a list of all known repositories.

  To only show the data that can be gathered quickly, use --fast.

* map

  Helps you keep track of your repositories, and the connections between them,
  by going out and looking at all the ones it can get to, and generating a
  Graphviz file displaying it all. If the `dot` command is available, it is
  used to display the file to your screen (using x11 backend). (To disable
  this display, specify --fast)

  This command only connects to hosts that the host it's run on can
  directly connect to. It does not try to tunnel through intermediate hosts.
  So it might not show all connections between the repositories in the network.

  Also, if connecting to a host requires a password, you might have to enter
  it several times as the map is being built.

  Note that this subcommand can be used to graph any git repository; it
  is not limited to git-annex repositories.

# UTILITY COMMANDS

* migrate [path ...]

  Changes the specified annexed files to use the default key-value backend
  (or the one specified with --backend). Only files whose content
  is currently available are migrated.

  Note that the content is also still available using the old key after
  migration. Use `git annex unused` to find and remove the old key.

  Normally, nothing will be done to files already using the new backend.
  However, if a backend changes the information it uses to construct a key,
  this can also be used to migrate files to use the new key format.

* reinject src dest

  Moves the src file into the annex as the content of the dest file.
  This can be useful if you have obtained the content of a file from
  elsewhere and want to put it in the local annex.

  Automatically runs fsck on dest to check that the expected content was
  provided.

  Example:

	git annex reinject /tmp/foo.iso foo.iso

* unannex [path ...]

  Use this to undo an accidental `git annex add` command. You can use
  `git annex unannex` to move content out of the annex at any point,
  even if you've already committed it.

  This is not the command you should use if you intentionally annexed a
  file and don't want its contents any more. In that case you should use
  `git annex drop` instead, and you can also `git rm` the file.

  In --fast mode, this command leaves content in the annex, simply making
  a hard link to it.

* uninit

  Use this to stop using git annex. It will unannex every file in the
  repository, and remove all of git-annex's other data, leaving you with a
  git repository plus the previously annexed files.

# PLUMBING COMMANDS

* pre-commit [path ...]

  Fixes up symlinks that are staged as part of a commit, to ensure they
  point to annexed content. Also handles injecting changes to unlocked
  files into the annex.

  This is meant to be called from git's pre-commit hook. `git annex init`
  automatically creates a pre-commit hook using this.

* fromkey key file

  This plumbing-level command can be used to manually set up a file
  in the git repository to link to a specified key.

* dropkey [key ...]

  This plumbing-level command drops the annexed data for the specified
  keys from this repository.

  This can be used to drop content for arbitrary keys, which do not need
  to have a file in the git repository pointing at them.

  Example:

	git annex dropkey SHA1-s10-7da006579dd64330eb2456001fd01948430572f2

* rekey [file key ...]
  
  This plumbing-level command is similar to migrate, but you specify
  both the file, and the new key to use for it.

  With --force, even files whose content is not currently available will
  be rekeyed. Use with caution.

# OPTIONS

* --force

  Force unsafe actions, such as dropping a file's content when no other
  source of it can be verified to still exist, or adding ignored files.
  Use with care.

* --fast

  Enables less expensive, but also less thorough versions of some commands.
  What is avoided depends on the command.

* --auto

  Enables automatic mode. Commands that get, drop, or move file contents
  will only do so when needed to help satisfy the setting of annex.numcopies.

* --quiet

  Avoid the default verbose display of what is done; only show errors
  and progress displays.

* --verbose

  Enable verbose display.

* --json

  Rather than the normal output, generate JSON. This is intended to be
  parsed by programs that use git-annex. Each line of output is a JSON
  object.

* --debug

  Show debug messages.

* --from=repository

  Specifies a repository that content will be retrieved from, or that
  should otherwise be acted on.

  It should be specified using the name of a configured remote.

* --to=repository

  Specifies a repository that content will be sent to.

  It should be specified using the name of a configured remote.

* --numcopies=n

  Overrides the `annex.numcopies` setting, forcing git-annex to ensure the
  specified number of copies exist.

* --trust=repository
* --semitrust=repository
* --untrust=repository

  Overrides trust settings for a repository. May be specified more than once.
  
  The repository should be specified using the name of a configured remote,
  or the UUID or description of a repository.

* --backend=name

  Specifies which key-value backend to use. This can be used when
  adding a file to the annex, or migrating a file. Once files
  are in the annex, their backend is known and this option is not
  necessary.

* --format=value

  Specifies a custom output format. The value is a format string, 
  in which '${var}' is expanded to the value of a variable. To right-justify
  a variable with whitespace, use '${var;width}' ; to left-justify
  a variable, use '${var;-width}'; to escape unusual characters in a variable,
  use '${escaped_var}'

  Also, '\\n' is a newline, '\\000' is a NULL, etc.

* -c name=value

  Used to override git configuration settings. May be specified multiple times.

# FILE MATCHING OPTIONS

These options can all be specified multiple times, and can be combined to
limit which files git-annex acts on.

Arbitrarily complicated expressions can be built using these options.
For example:

	--exclude '*.mp3' --and --not -( --in=usbdrive --or --in=archive -)

The above example prevents git-annex from working on mp3 files whose
file contents are present at either of two repositories.

* --exclude=glob

  Skips files matching the glob pattern. The glob is matched relative to
  the current directory. For example:

	--exclude='*.mp3' --exclude='subdir/*'

* --include=glob

  Skips files not matching the glob pattern.  (Same as --not --exclude.)
  For example, to include only mp3 and ogg files:

	--include='*.mp3' --or --include='*.ogg'

* --in=repository

  Matches only files that git-annex believes have their contents present
  in a repository. Note that it does not check the repository to verify
  that it still has the content.

  The repository should be specified using the name of a configured remote,
  or the UUID or description of a repository. For the current repository,
  use --in=here

* --copies=number

  Matches only files that git-annex believes to have the specified number
  of copies, or more. Note that it does not check remotes to verify that
  the copies still exist.

* --inbackend=name

  Matches only files whose content is stored using the specified key-value
  backend.

* --not

  Inverts the next file matching option. For example, to only act on
  mp3s, use: --not --exclude='*.mp3'

* --and

  Requires that both the previous and the next file matching option matches.
  The default.

* --or

  Requires that either the previous, or the next file matching option matches.

* -(

  Opens a group of file matching options.

* -)

  Closes a group of file matching options.

# CONFIGURATION

Like other git commands, git-annex is configured via `.git/config`.
Here are all the supported configuration settings.

* `annex.uuid`

  A unique UUID for this repository (automatically set).

* `annex.numcopies`

  Number of copies of files to keep across all repositories. (default: 1)

* `annex.backends`

  Space-separated list of names of the key-value backends to use. 
  The first listed is used to store new files by default. 

* `annex.diskreserve`

  Amount of disk space to reserve. Disk space is checked when transferring
  content to avoid running out, and additional free space can be reserved
  via this option, to make space for more important content (such as git
  commit logs). Can be specified with any commonly used units, for example,
  "0.5 gb" or "100 KiloBytes"

  The default reserve is 1 megabyte.

* `annex.queuesize`

  git-annex builds a queue of git commands, in order to combine similar
  commands for speed. By default the size of the queue is limited to
  10240 commands; this can be used to change the size. If you have plenty
  of memory and are working with very large numbers of files, increasing
  the queue size can speed it up.

* `annex.bloomcapacity`

  The `git annex unused` command uses a bloom filter to determine
  what data is no longer used. The default bloom filter is sized to handle
  up to 500000 keys. If your repository is larger than that,
  you can adjust this to avoid `git annex unused` not noticing some unused
  data files. Increasing this will make `git-annex unused` consume more memory;
  run `git annex status` for memory usage numbers.

* `annex.bloomaccuracy`

  Adjusts the accuracy of the bloom filter used by
  `git annex unused`. The default accuracy is 1000 -- 
  1 unused file out of 1000 will be missed by `git annex unused`. Increasing
  the accuracy will make `git annex unused` consume more memory;
  run `git annex status` for memory usage numbers.

* `annex.version`

  Automatically maintained, and used to automate upgrades between versions.

* `annex.sshcaching`

  By default, git-annex caches ssh connections
  (if built using a new enough ssh). To disable this, set to `false`.

* `annex.alwayscommit`

  By default, git-annex automatically commits data to the git-annex branch
  after each command is run. To disable these commits,
  set to `false`. Then data will only be committed when
  running `git annex merge` (or by automatic merges) or `git annex sync`.

* `remote.<name>.annex-cost`

  When determining which repository to
  transfer annexed files from or to, ones with lower costs are preferred.
  The default cost is 100 for local repositories, and 200 for remote
  repositories.

* `remote.<name>.annex-cost-command`

  If set, the command is run, and the number it outputs is used as the cost.
  This allows varying the cost based on eg, the current network. The
  cost-command can be any shell command line.

* `remote.<name>.annex-start-command`

  A command to run when git-annex begins to use the remote. This can
  be used to, for example, mount the directory containing the remote.

  The command may be run repeatedly in multiple git-annex processes
  are running concurrently.

* `remote.<name>.annex-stop-command`

  A command to run when git-annex is done using the remote.

  The command will only be run once *all* running git-annex processes
  are finished using the remote.

* `remote.<name>.annex-ignore`

  If set to `true`, prevents git-annex
  from using this remote by default. (You can still request it be used
  by the --from and --to options.)

  This is, for example, useful if the remote is located somewhere
  without git-annex-shell. (For example, if it's on GitHub).
  Or, it could be used if the network connection between two
  repositories is too slow to be used normally.

* `remote.<name>.annexUrl`

  Can be used to specify a different url than the regular `remote.<name>.url`
  for git-annex to use when talking with the remote. Similar to the `pushUrl`
  used by git-push.

* `remote.<name>.annex-uuid`

  git-annex caches UUIDs of remote repositories here.

* `remote.<name>.annex-trustlevel`

  Configures a local trust level for the remote. This overrides the value
  configured by the trust and untrust commands. The value can be any of
  "trusted", "semitrusted" or "untrusted".

* `remote.<name>.annex-ssh-options`

  Options to use when using ssh to talk to this remote.

* `remote.<name>.annex-rsync-options`

  Options to use when using rsync
  to or from this remote. For example, to force ipv6, and limit
  the bandwidth to 100Kbyte/s, set it to "-6 --bwlimit 100"

* `remote.<name>.annex-web-options`

  Options to use when using wget or curl to download a file from the web.
  (wget is always used in preference to curl if available).
  For example, to force ipv4 only, set it to "-4"

* `remote.<name>.annex-bup-split-options`

  Options to pass to bup split when storing content in this remote.
  For example, to limit the bandwidth to 100Kbye/s, set it to "--bwlimit 100k"
  (There is no corresponding option for bup join.)

* `annex.ssh-options`, `annex.rsync-options`, `annex.web-options, `annex.bup-split-options`

  Default ssh, rsync, wget/curl, and bup options to use if a remote does not
  have specific options.

* `remote.<name>.buprepo`

  Used by bup special remotes, this configures
  the location of the bup repository to use. Normally this is automaticaly
  set up by `git annex initremote`, but you can change it if needed.

* `remote.<name>.directory`

  Used by directory special remotes, this configures
  the location of the directory where annexed files are stored for this
  remote. Normally this is automaticaly set up by `git annex initremote`,
  but you can change it if needed.

* `remote.<name>.s3`

  Used to identify Amazon S3 special remotes.
  Normally this is automaticaly set up by `git annex initremote`.

# CONFIGURATION VIA .gitattributes

The key-value backend used when adding a new file to the annex can be
configured on a per-file-type basis via `.gitattributes` files. In the file,
the `annex.backend` attribute can be set to the name of the backend to
use. For example, this here's how to use the WORM backend by default,
but the SHA1 backend for ogg files:

	* annex.backend=WORM
	*.ogg annex.backend=SHA1

The numcopies setting can also be configured on a per-file-type basis via
the `annex.numcopies` attribute in `.gitattributes` files.
For example, this makes two copies be needed for wav files:

	*.wav annex.numcopies=2

# FILES

These files are used by git-annex, in your git repository:

`.git/annex/objects/` contains the annexed file contents that are currently
available. Annexed files in your git repository symlink to that content.

# SEE ALSO

Most of git-annex's documentation is available on its web site, 
<http://git-annex.branchable.com/>

If git-annex is installed from a package, a copy of its documentation
should be included, in, for example, `/usr/share/doc/git-annex/`

# AUTHOR

Joey Hess <joey@kitenet.net>

<http://git-annex.branchable.com/>

Warning: Automatically converted into a man page by mdwn2man. Edit with care