-help : show this help
-hist : show module history
-show_valid_opts : list valid options
-ver : show current version
required:
-build_root BUILD_ROOT : root directory to use for git and building
other options:
-abin ABIN : specify AFNI binary install directory
default -abin <directory containing afni_proc.py>
e.g. -abin $HOME/my_new_abin
When this option is given, any installation of the compiled binaries
will be placed into this ABIN directory. If this option is not
given, it will be determined by `which afni_proc.py`.
If this directory does not exist, it will be created upon install.
-backup_method BACK_METH : specify how to perform the backup
default -backup_method rsync
e.g. -backup_method mv
This option is used to specify how a backup of ABIN is made. It
should be one of:
mv : apply the Unix 'mv' command
+ Benefit: ABIN is really cleaned, and will not contain
any removed files. This method should be faster.
rsync : apply the Unix 'rsync' command
(this is the default method)
+ Benefit: ABIN is preserved during the backup process.
Even if the program is terminated while making the
backup, ABIN will be maintained.
+ Benefit: old ABIN files are removed.
So old files do not accumulate.
If some file or program is no longer built and
distributed, it will not linger in the ABIN.
After the backup stage, ABIN is emptied before
repopulating it with a new install.
rsync_preserve : use 'rsync', but do not remove old files
+ Benefit: ABIN is preserved.
+ Benefit: old ABIN files are never removed.
So old files accumulate over time.
If some file or program is no longer built and
distributed, it will linger in the ABIN.
See also -do_backup.
-cc_path PATH/TO/COMPILER : specify the path to a C compiler to use
e.g. -cc_path /usr/local/bin/gcc-14
e.g. -cc_path NONE
If a Makefile uses LOCAL_CC_PATH (most do not), one can pass an
alternative to what is default in the Makefile.
For example, Makefile.macos_12_x86_64 uses /usr/local/bin/gcc-13.
This option can be used to override that compiler path as the user
sees fit, such as with /usr/local/bin/gcc-14 or even /usr/bin/clang.
* If this option is not used and the default compiler does not exist,
the program will attempt to find an alternate compiler with a
different version number.
* Use NONE to forcibly use the Makefile default, even if it does not
exist.
-clean_root yes/no : specify whether to clean up the build_root
default -clean_root yes
e.g. -clean_root no
If 'no' is specified, the git directory will not be updated and the
build_src directory will not be remade.
-do_backup yes/no : specify whether to back up abin before install
default -do_backup yes
e.g. -do_backup no
By default backup will be made whenever a full installation is done
(of both AFNI binaries and atlases). The backup (of ABIN, specified
by -abin) will be placed under the BUILD_ROOT directory (specified
by -build_root).
The backup is made by moving the full contents of the abin, so that
AFNI updates that remove files or programs will indeed remove them.
If a full install will not be done, a backup will not be made.
One may use -backup_method to control the command used to make the
backup.
See also -backup_method.
-do_install yes/no : specify whether to install compiled binaries
default -do_install yes
e.g. -do_install no
By default, compiled AFNI binaries and atlases will be installed
into the ABIN directory given by -abin (or else from the $PATH).
If 'no' is specified, no installation will take place (and no backup
will be made).
See also -abin, -do_backup.
-git_branch BRANCH : specify a branch to checkout in git
default -git_branch master
e.g. -git_branch some_stupid_branch
This will checkout and pull the branch. To build of the most recent
version of a branch (and not the most recent tag), include:
-git_tag NONE
Unless using '-git_update no', the current branch will be updated
(default master), to make sure any relevant tag will exist.
Note that precise tags generally refer to a specific branch. So it
is easy to specify a branch and a tag that is not actually associated
with that branch.
See also -git_tag.
-git_tag TAG : specify a tag to checkout in git
default -git_tag LAST_TAG
e.g. -git_tag NONE
This will lead to 'git checkout TAG', of some sort, depending:
LAST_TAG : checkout most recent (annotated) AFNI_XX.X.XX tag.
(annotated tags come from official AFNI builds)
NONE : do not checkout any specific tag
(use this to build from the current branch state)
By default, the most recent tag is checked out (for the purpose of
aligning the build with AFNI releases). To build off of the most
recent state of a branch, use "-git_tag NONE".
The LAST_TAG option will generally imply the most recent "official"
AFNI tag based on the master branch.
-git_update yes/no : specify whether to update git repo
default -git_update yes
e.g. -git_update no
If 'no' is specified, the git/afni/src tree must already exist, and
nothing will be done to it. This option cannot be used with
-git_branch or -git_tag.
-make_flags VAR=VAL VAR=VAL : provide list of extra make flags
e.g. -make_flags INSTALL_PREREQ=
e.g. -make_flags INSTALL_PREREQ=suma_gts SYSTEM_NAME=macos_13_ARM
Pass a list of flags to the make process, overriding what might be
set in the Makefile.
The passed parameters to -make_flags should be a list in the form
VARIABLE=VALUE. Multiple such parameters can be passed in a single
option use.
-make_target TARGET : specify target for make command
default -make_target itall
e.g. -make_target totality
e.g. -make_target afni
When the 'make' command is run under build_src, use the given target.
Since an individual program make would probably be done directly on
the command line (rather than using this program), the most typical
reason to do this might be to save disk space. Using totality
(instead of itall) would clean up after the make.
-makefile MAKEFILE : specify an alternate Makefile to build from
default -makefile Makefile.PACKAGE (for the given PACKAGE)
e.g. -makefile my.better.makefile
This option is a mechanism for specifying a Makefile that is not
(currently) part of the AFNI distribution.
-package PACKAGE : specify the desired package to build
e.g. -package linux_centos_7_64
The package will imply a Makefile to use, Makefile.PACKAGE.
It will also be the name of the output binary directory.
-prep_only : prepare to but do not run (c)make
e.g. -prep_only
This is for testing or for practice.
Do everything leading up to running cmake or make commands,
but do not actually run them (make/cmake). This still requires a
git tree, but using "-git_update no" is okay.
-run_cmake yes/no : choose whether to run a cmake build
default: -run_cmake no
e.g. : -run_cmake yes
If requested, run a cmake build under the build_cmake directory.
-run_make yes/no : choose whether to run a make build
default: -run_cmake yes
e.g. : -run_cmake no
By default, a make build will be run. Use this option to specify
not to.
-update_atlases yes/no : update atlases, even if the package exists
default: -update_atlases yes
e.g. : -update_atlases no
By default, even if the atlases directory exists (afni_atlases_dist),
it will be updated. Use this option to avoid a new download.
If -clean_root is 'no', atlases will not be updated.
-update_niivue yes/no : update NiiVue, even if the package exists
default: -update_niivue yes
e.g. : -update_niivue no
By default, even if NiiVue exists, it will be updated. Use this
option to avoid a new download.
If -clean_root is 'no', NiiVue will not be updated.
-verb LEVEL : set the verbosity level (default 1)
e.g. -verb 2
Specify how verbose the program should be, from 0=quiet to 4=max.
As is typical, the default level is 1.
R Reynolds sometime 2023
