bv_env¶
bv_env program¶
The bv_env program sets up paths to run all programs from a build tree or binary package installation of software built or installed via the brainvisa-cmake environment.
It sets basically PATH, LD_LIBRARY_PATH, PYTHONPATH and BRAINVISA_SHARE environment variables, and saves their previous values in BRAINVISA_UNENV_* variables.
When run with no arguments, bv_env just prints the environment it would set.
When run with arguments, bv_env will run the commandline specified as arguments, in the bv_env environment.
/home/myself/brainvisa_install/bin/bv_env anatomist /home/myself/data/mri.nii /home/myself/data/brain_mesh.gii
The environment is set only duing the command execution time, it does not modify shell variables from the calling program or shell.
The program is relocatable, this means that if you move the install tree after it is installed, bv_env will find out from where it is run and adapt, so it will still be valid.
bv_env.sh, bv_env.csh, bv_env.bat scripts¶
These scripts do the same as the bv_env program, except that they do not run a program on-the-fly, but change the calling shell environment variables. As it depends on the shell type used, there are several scripts for sh/bash, csh/tcsh, or windows DOS shells.
We have to admit that currently we only use bash shells and the other scripts are mostly untested.
In Unix shells (sh, bash, csh, tcsh), to actually modify the running environment, the scripts have to be sourced, not just run. Ex:
. /home/myself/brainvisa_install/bin/bv_env.sh
or:
source /home/myself/brainvisa_install/bin/bv_env.sh
will modify the calling shell, whereas:
/home/myself/brainvisa_install/bin/bv_env.sh
will just appear to no nothing (it will modify variables internally during the script execution, but the calling shell will not be modified).
The programs are relocatable, this means that if you move the install tree after it is installed, bv_env.* scripts will find out from where it is run and adapt, so it will still be valid.
However to find out where they are run from, the scripts need to access the shell commands history, so the above commands will work in an interactive shell, but not from within a script or .bashrc configuration script.
To overcome this problem, she bv_env.sh script can be passed an argument, which is the build / install directory location:
. /home/myself/brainvisa_install/bin/bv_env.sh /home/myself/brainvisa_install
bv_unenv¶
If you need to run an “external” program, a program not part of the BrainVisa package, from a program within the BrainVisa environment, it may cause environment and libraries conflict problems, because BV programs need some libraries installed within the installation directory and environment, but “external” programs need the system versions.
When running such a program, it is possible to “undo” the environment setup of bv_env, using the bv_unenv program.
It otherwise works the same way.
The bv_unenv.sh script is the equivalent to undo bv_env.sh script.