Add quickstart guide
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---
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title: "Docs"
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description: "Documentation for users of jungle machines"
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date: 2023-09-15
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---
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If this is the first time you use any of the jungle machines with NixOS, follow
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the [quick start guide](quickstart).
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---
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title: "Quick start"
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date: 2023-09-15
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---
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This documentation will guide you on how to build custom packages of software
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and use them in the jungle machines. It has been designed to reduce the friction
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from users coming from module systems.
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You should be able to access the jungle machines, otherwise [request
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access](/access).
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## Changes from other HPC machines
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Users of other machines have been using the Lmod tool (module load ...) to add
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or remove programs from their environment, as well as manually building their
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own software for too many years.
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While we cannot prevent users from continuing to use this tedious mechanism, we
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have designed the jungle machines to be much easier to operate by using the nix
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package manager.
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### Freedom to install packages
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When a user wanted to install a package, it was forced to either do it on its
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own directory, or request a system administrator to install it in a shared
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directory, so other users can also use that package.
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This situation is gone, each user can install any package of software by
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themselves, without requiring any other authorization. When two users request
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the same package, the same copy will be provided.
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A new package will be downloaded if it is available (someone already built it)
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or will be built from source on demand.
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### No changes over time
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All users retain the same versions of the packages they request until they
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decide to update them.
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## Using nix to manage packages
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In this chapter we show how to install packages and enter a development shell to
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build new programs from source. The examples are done from the hut machine,
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read [this page](/access) to request access.
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### Installing binaries
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To temporarily install new packages, use:
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```text
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hut% nix shell jungle#gcc jungle#cowsay jungle#ovni
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```
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Notice that the packages are described as two parts divided by the `#` symbol.
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The first part defines where to take the package from and the second part is
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the name of the package. For now we will use `jungle#<package>`. You can find
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many more packages here:
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<https://search.nixos.org/packages>
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You will now enter a new shell, where those requested package **binaries are
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available in $PATH**:
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```text
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hut% cowsay hello world
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_____________
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< hello world >
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-------------
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\ ^__^
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\ (oo)\_______
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(__)\ )\/\
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||----w |
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|| ||
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hut% ovniver
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LD_LIBRARY_PATH not set
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libovni: build v1.11.0 (a7103f8), dynamic v1.11.0 (a7103f8)
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hut% gcc --version
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gcc (GCC) 13.3.0
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Copyright (C) 2023 Free Software Foundation, Inc.
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This is free software; see the source for copying conditions. There is NO
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warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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```
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### Building programs
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The above method only loads new binaries in the `$PATH`. If we try to build a
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program that includes headers or links with a library, it will fail to find
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them:
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```text
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hut$ cat test.c
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#include <ovni.h>
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int main()
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{
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ovni_version_check();
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return 0;
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}
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hut% gcc test.c -lovni -o test
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test.c:1:10: fatal error: ovni.h: No such file or directory
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1 | #include <ovni.h>
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| ^~~~~~~~
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compilation terminated.
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```
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We could manually add the full path to the ovni include directory with `-I` and
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the libraries with `-L`, but there is a tool that already perform these steps
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automatically for us, `nix develop`.
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Let's go back to our original shell first, where those packages are not
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available anymore:
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```
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hut% ps
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PID TTY TIME CMD
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2356260 pts/1 00:00:01 zsh
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2457268 pts/1 00:00:00 zsh
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2457297 pts/1 00:00:00 ps
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hut% exit
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hut% ovniver
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ovniver: command not found
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```
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### Creating a flake.nix
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To define which packages we want, we will write a small file that list them, a
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flake.nix file.
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First, we will create a new directory where we are going to be working:
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```
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hut% mkdir example
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hut% cd exmple
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```
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Then place this flake.nix file:
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```nix
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{
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inputs.jungle.url = "jungle";
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outputs = { self, jungle }:
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let
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pkgs = jungle.outputs.packages.x86_64-linux;
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in {
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devShells.x86_64-linux.default = pkgs.mkShell {
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pname = "devshell";
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buildInputs = with pkgs; [
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ovni gcc cowsay # more packages here...
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];
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};
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};
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}
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```
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Now enter the shell with:
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```
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hut% nix develop
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warning: creating lock file '/home/Computational/rarias/example/flake.lock':
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• Added input 'jungle':
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'path:/nix/store/27srv8haj6vv4ywrbmw0a8vds561m8rq-source?lastModified=1739479441&narHash=sha256-Kgjs8SO1w9NbPBu8ghwzCxYJ9kvWpoQOT%2BXwPvA9DcU%3D&rev=76396c0d67ef0cf32377d5c1894bb695293bca9d' (2025-02-13)
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• Added input 'jungle/agenix':
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'github:ryantm/agenix/f6291c5935fdc4e0bef208cfc0dcab7e3f7a1c41?narHash=sha256-b%2Buqzj%2BWa6xgMS9aNbX4I%2BsXeb5biPDi39VgvSFqFvU%3D' (2024-08-10)
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• Added input 'jungle/agenix/darwin':
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'github:lnl7/nix-darwin/4b9b83d5a92e8c1fbfd8eb27eda375908c11ec4d?narHash=sha256-gzGLZSiOhf155FW7262kdHo2YDeugp3VuIFb4/GGng0%3D' (2023-11-24)
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• Added input 'jungle/agenix/darwin/nixpkgs':
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follows 'jungle/agenix/nixpkgs'
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• Added input 'jungle/agenix/home-manager':
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'github:nix-community/home-manager/3bfaacf46133c037bb356193bd2f1765d9dc82c1?narHash=sha256-7ulcXOk63TIT2lVDSExj7XzFx09LpdSAPtvgtM7yQPE%3D' (2023-12-20)
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• Added input 'jungle/agenix/home-manager/nixpkgs':
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follows 'jungle/agenix/nixpkgs'
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• Added input 'jungle/agenix/nixpkgs':
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follows 'jungle/nixpkgs'
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• Added input 'jungle/agenix/systems':
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'github:nix-systems/default/da67096a3b9bf56a91d16901293e51ba5b49a27e?narHash=sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768%3D' (2023-04-09)
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• Added input 'jungle/bscpkgs':
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'git+https://git.sr.ht/~rodarima/bscpkgs?ref=refs/heads/master&rev=6782fc6c5b5a29e84a7f2c2d1064f4bcb1288c0f' (2024-11-29)
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• Added input 'jungle/bscpkgs/nixpkgs':
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follows 'jungle/nixpkgs'
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• Added input 'jungle/nixpkgs':
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'github:NixOS/nixpkgs/9c6b49aeac36e2ed73a8c472f1546f6d9cf1addc?narHash=sha256-i/UJ5I7HoqmFMwZEH6vAvBxOrjjOJNU739lnZnhUln8%3D' (2025-01-14)
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hut$
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```
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Notice that long list of messages is Nix creating a new flake.lock file with the
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current state of the packages. Next invocations will use the same packages as
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described by the lock file.
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### Building a program from nix develop
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Now let's try again building our test program:
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```text
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hut$ cat test.c
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#include <ovni.h>
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int main()
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{
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ovni_version_check();
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return 0;
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}
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hut$ gcc test.c -o test -lovni
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hut$ ldd test
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linux-vdso.so.1 (0x00007ffff7fc4000)
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libovni.so.1 => /nix/store/sqk972akjv0q8dchn8ccjln2llzyyfd0-ovni-1.11.0/lib/libovni.so.1 (0x00007ffff7fab000)
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libc.so.6 => /nix/store/nqb2ns2d1lahnd5ncwmn6k84qfd7vx2k-glibc-2.40-36/lib/libc.so.6 (0x00007ffff7db2000)
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/nix/store/nqb2ns2d1lahnd5ncwmn6k84qfd7vx2k-glibc-2.40-36/lib/ld-linux-x86-64.so.2 => /nix/store/nqb2ns2d1lahnd5ncwmn6k84qfd7vx2k-glibc-2.40-36/lib64/ld-linux-x86-64.so.2 (0x00007ffff7fc6000)
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hut$ ./test
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```
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Now the ovni.h header and the libovni library are found and the program is
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successfully built, linked and executed.
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You can add more packages as needed in your flake.nix:
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```nix
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buildInputs = with pkgs; [
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ovni gcc cowsay # more packages here...
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];
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```
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Make sure you exit the develop shell first, and then enter again with `nix
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develop`.
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## Remember
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- `nix shell` places binaries in the `$PATH`.
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- `nix develop` enters a development shell where both binaries and the libraries
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and includes are available so you can build new programs.
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@ -3,32 +3,38 @@ languageCode = 'en-us'
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title = 'The jungle'
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theme = 'PaperMod'
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[[menu.main]]
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identifier = "doc"
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name = "Docs"
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url = "/doc/"
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weight = 10
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[[menu.main]]
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identifier = "grafana"
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name = "Grafana"
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url = "/grafana/"
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weight = 10
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weight = 20
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[[menu.main]]
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identifier = "Git"
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name = "Git"
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url = "/git/"
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weight = 20
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weight = 30
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[[menu.main]]
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identifier = "Lists"
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name = "Lists"
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url = "/lists/"
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weight = 30
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weight = 40
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[[menu.main]]
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identifier = "Paste"
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name = "Paste"
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url = "/paste/"
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weight = 40
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weight = 50
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[[menu.main]]
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identifier = "Posts"
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name = "Posts"
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url = "/posts/"
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weight = 50
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weight = 60
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