One of the most commonly used options to ./configure is --prefix, it is used to define the directory that will host all the installed files (or the “prefix” in their final absolute file name). For example, when you are using a server and you don’t have administrator or root access. In this example scenario, if you don’t use the --prefix option, you won’t be able to install the built files and thus access them from anywhere without having to worry about where they are installed. However, once you prepare your startup file to look into the proper place (as discussed thoroughly below), you will be able to easily use this option and benefit from any software you want to install without having to ask the system administrators or install and use a different version of a software that is already installed on the server.
The most basic way to run an executable is to explicitly write its full
file name (including all the directory information) and run it. One example
is running the configuration script with the
command (see Quick start). By giving a specific directory (the
current directory or ./), we are explicitly telling the shell to
look in the current directory for an executable file named
‘configure’. Directly specifying the directory is thus useful for
executables in the current (or nearby) directories. However, when the
program (an executable file) is to be used a lot, specifying all those
directories will become a significant burden. For example, the ls
executable lists the contents in a given directory and it is (usually)
installed in the /usr/bin/ directory by the operating system
maintainers. So each time you want to use it you would have to run the
following command (which is very inconvenient, both in writing and in
remembering the various directories).
To address this problem, we have the PATH environment variable. To understand it better, we will start with a short introduction to the shell variables. Shell variable values are basically treated as strings of characters. For example, it doesn’t matter if the value is a name (string of alphabetic characters) or a number (string of numeric characters). You can define a variable and a value for it by running
$ myvariable1=a_test_value $ myvariable2="a test value"
As you see above, if the value contains white space characters, you have to put the whole value (including white space characters) in double quotes ("). You can see the value it represents by running
$ echo $myvariable1 $ echo $myvariable2
If a variable has no value or it wasn’t defined, the last command will only print an empty line. A variable defined like this will be known as long as this shell or terminal is running. Other terminals will have no idea it existed. The main advantage of shell variables is that if they are exported44, subsequent programs that are run within that shell can access their value. So by changing their value, you can change the “environment” of a program which uses them. The shell variables which are accessed by programs are therefore known as “environment variables”45. You can see the full list of exported variables that your shell recognizes by running:
HOME is one commonly used environment variable, it is any user’s (the one that is logged in) top directory. Try finding it in the command above. It is used so often that the shell has a special expansion (alternative) for it: ‘~’. Whenever you see file names starting with the tilde sign, it actually represents the value to the HOME environment variable, so ~/doc is the same as $HOME/doc.
Another one of the most commonly used environment variables is PATH,
it is a list of directories to search for executable names. Its value is a
list of directories (separated by a colon, or ‘:’). When the address
of the executable is not explicitly given (like ./configure above),
the system will look for the executable in the directories specified by
PATH. If you have a computer nearby, try running the following
command to see which directories your system will look into when it is
searching for executable (binary) files, one example is printed here
(notice how /usr/bin, in the ls example above, is one of the
$ echo $PATH /usr/local/sbin:/usr/local/bin:/usr/bin
By default PATH usually contains system-wide directories, which are readable (but not writable) by all users, like the above example. Therefore if you don’t have root (or administrator) access, you need to add another directory to PATH which you actually have write access to. The standard directory where you can keep installed files (not just executables) for your own user is the ~/.local/ directory. The names of hidden files start with a ‘.’ (dot), so it will not show up in your common command-line listings, or on the graphical user interface. You can use any other directory, but this is the most recognized.
The top installation directory will be used to keep all the package’s
components: programs (executables), libraries, include (header) files,
shared data (like manuals), or configuration files (see Review of library fundamentals for a thorough introduction to headers and
linking). So it commonly has some of the following sub-directories for each
class of installed components respectively: bin/, lib/,
include/ man/, share/, etc/. Since the
PATH variable is only used for executables, you can add the
~/.local/bin directory (which keeps the executables/programs or more
generally, “binary” files) to PATH with the following command. As
defined below, first the existing value of PATH is used, then your
given directory is added to its end and the combined value is put back in
PATH (run ‘
$ echo $PATH’ afterwards to check if it was
Any executable that you installed in ~/.local/bin will now be usable without having to remember and write its full address. However, as soon as you leave/close your current terminal session, this modified PATH variable will be forgotten. Adding the directories which contain executables to the PATH environment variable each time you start a terminal is also very inconvenient and prone to errors. Fortunately, there are standard ‘startup files’ defined by your shell precisely for this (and other) purposes. There is a special startup file for every significant starting step:
These startup scripts are called when your whole system starts (for example after you turn on your computer). Therefore you need administrator or root privileges to access or modify them.
If you are using (GNU) Bash as your shell, the commands in this file are run once every time you log in to your account.
If you are using (GNU) Bash as your shell, the commands here will be run each time you start a terminal (for example, when you open your terminal emulator in the graphic user interface).
For security reasons, it is highly recommended to directly type in your
HOME directory value by hand in startup files instead of using
variables. So in the following, let’s assume your user name is
‘name’ (so ~ may be replaced with /home/name). To add
~/.local/bin to your PATH automatically on any startup file,
you have to “export” the new value of
PATH in the startup file
that is most relevant to you by adding this line:
Now that you know your system will look into ~/.local/bin for
executables, you can tell Gnuastro’s configure script to install everything
in the top ~/.local directory using the --prefix
option. When you subsequently run
$ make install, all the
install-able files will be put in their respective directory under
~/.local/ (the executables in ~/.local/bin, the compiled
library files in ~/.local/lib, the library header files in
~/.local/include and so on, to learn more about these different
files, please see Review of library fundamentals). Note that tilde
(‘~’) expansion will not happen if you put a ‘=’ between
--prefix and ~/.local46, so we have avoided
the = character here which is optional in GNU-style options, see
$ ./configure --prefix ~/.local
You can install everything (including libraries like GSL, CFITSIO, or
WCSLIB which are Gnuastro’s mandatory dependencies, see Mandatory dependencies) locally by configuring them as above. However, recall that
PATH is only for executable files, not libraries and that
libraries can also depend on other libraries. For example WCSLIB depends on
CFITSIO and Gnuastro needs both. Therefore, when you installed a library in
a non-recognized directory, you have to guide the program that depends on
them to look into the necessary library and header file directories. To do
that, you have to define the
environment variables respectively. This can be done while calling
./configure as shown below:
$ ./configure LDFLAGS=-L/home/name/.local/lib \ CPPFLAGS=-I/home/name/.local/include \ --prefix ~/.local
It can be annoying/buggy to do this when configuring every software that
depends on such libraries. Hence, you can define these two variables in the
most relevant startup file (discussed above). The convention on using these
variables doesn’t include a colon to separate values (as
PATH-like variables do), they use white space characters and each
value is prefixed with a compiler option47: note
the -L and -I above (see Options), for -I
see Headers, and for -L, see Linking. Therefore we
have to keep the value in double quotation signs to keep the white space
characters and adding the following two lines to the startup file of
export LDFLAGS="$LDFLAGS -L/home/name/.local/lib" export CPPFLAGS="$CPPFLAGS -I/home/name/.local/include"
Dynamic libraries are linked to the executable every time you run a program
that depends on them (see Linking to fully understand this important
concept). Hence dynamic libraries also require a special path variable
LD_LIBRARY_PATH (same formatting as
use programs that depend on these libraries, you need to add
~/.local/lib to your
LD_LIBRARY_PATH environment variable
by adding the following line to the relevant start-up file:
If you also want to access the Info (see Info) and man pages (see
Man pages) documentations add ~/.local/share/info and
~/.local/share/man to your
MANPATH environment variables
A final note is that order matters in the directories that are searched for all the variables discussed above. In the examples above, the new directory was added after the system specified directories. So if the program, library or manuals are found in the system wide directories, the user directory is no longer searched. If you want to search your local installation first, put the new directory before the already existing list, like the example below.
This is good when a library, for example CFITSIO, is already present on the system, but the system-wide install wasn’t configured with the correct configuration flags (see CFITSIO), or you want to use a newer version and you don’t have administrator or root access to update it on the whole system/server. If you update LD_LIBRARY_PATH by placing ~/.local/lib first (like above), the linker will first find the CFITSIO you installed for yourself and link with it. It thus will never reach the system-wide installation.
There are important security problems with using local installations first:
all important system-wide executables and libraries (important executables
cp, or libraries like the C library) can be
replaced by non-secure versions with the same file names and put in the
customized directory (~/.local in this example). So if you choose to
search in your customized directory first, please be sure to keep it
clean from executables or libraries with the same names as important system
programs or libraries.
Summary: When you are using a server which doesn’t give you administrator/root access AND you would like to give priority to your own built programs and libraries, not the version that is (possibly already) present on the server, add these lines to your startup file. See above for which startup file is best for your case and for a detailed explanation on each. Don’t forget to replace ‘/YOUR-HOME-DIR’ with your home directory (for example ‘/home/your-id’):
export PATH="/YOUR-HOME-DIR/.local/bin:$PATH" export LDFLAGS="-L/YOUR-HOME-DIR/.local/lib $LDFLAGS" export MANPATH="/YOUR-HOME-DIR/.local/share/man/:$MANPATH" export CPPFLAGS="-I/YOUR-HOME-DIR/.local/include $CPPFLAGS" export INFOPATH="/YOUR-HOME-DIR/.local/share/info/:$INFOPATH" export LD_LIBRARY_PATH="/YOUR-HOME-DIR/.local/lib:$LD_LIBRARY_PATH"
Afterwards, you just need to add an extra --prefix=/YOUR-HOME-DIR/.local to the ./configure command of the software that you intend to install. Everything else will be the same as a standard build and install, see Quick start.
$ export myvariable=a_test_value
instead of the simpler case in the text
You can use shell variables for other actions too, for example to temporarily keep some names or run loops on some files.
If you insist on using ‘=’, you can use --prefix=$HOME/.local.
These variables are ultimately used as options while building the programs, so every value has be an option name followed be a value as discussed in Options.
Info has the
following convention: “If the value of
INFOPATH ends with a
colon [or it isn’t defined] ..., the initial list of directories is
constructed by appending the build-time default to the value of
INFOPATH.” So when installing in a non-standard directory and if
INFOPATH was not initially defined, add a colon to the end of
INFOPATH as shown below, otherwise Info will not be able to find
system-wide installed documentation:
INFOPATH=$INFOPATH:/home/name/.local/share/info:' >> ~/.bashrc
Note that this is only an internal convention of Info, do not use it for other