Perl interface to manipulate BigWig and BigBeg files (for genomics)
This will be used to package VEP : uttps://www.ensembl.org/info/docs/tools/vep/script/vep_download.html
For that, only kent version 335 works at the moment.
For this commit, 2 commits for kent are needed
- e027a5d836 : packaging kent header
- 2b2c6f4c28 : enabling patches in kent
t/css-dom.t was deactivated because it failed due to deprecated syntax. This
commit uses an upstream patch to fix the syntax and activate the test again.
Update patch that supports NIX_SSL_CERT_FILE env variable so it's
compatible with LWP::Protocol::https 6.11
The new patch does not handle SSL_CERT_FILE or default cert store paths
as this is managed by IO::Socket::SSL.
When specifying the `builder` attribute in `stdenv.mkDerivation`, this
will be effectively transformed into
builtins.derivation {
builder = stdenv.shell;
args = [ "-e" builder ];
}
This also means that `default-builder.sh` is never sourced and as a
result it's not guaranteed that `$NIX_ATTRS_SH_FILE` is set to a correct
location[1].
Also, we need to source `.attrs.sh` to source `$stdenv`. So, the
following is done now:
* If `$NIX_ATTRS_SH_FILE` points to a correct location, then use it.
Directly using `.attrs.sh` is problematic for `nix-shell(1)` usage
(see previous commit for more context), so prefer the environment
variable if possible.
* Otherwise, if `.attrs.sh` exists, then use it. See [1] for when this
can happen.
* If neither applies, it can be assumed that `__structuredAttrs` is
turned off and thus nothing needs to be done.
[1] It's possible that it doesn't exist at all - in case of Nix 2.3 or
it can point to a wrong location on older Nix versions with a bug in
`__structuredAttrs`.
The jpeg `configure` script fails to detect clang as a functioning C
compiler because it uses a test with a `main` that returns an implicit
`int`, which results in an error with clang 16.
The motivation behind this is wanting to reduce the reverse closure size of
texlive.
When internationalizing tex files, Po4a attempts to follow included files. In
order to find the correct files, po4a uses texlive's file-finding utility
kpsewhich. This commit replaces texlive with a tiny shell script, which is
precisely good enough to run the tests.
This does not change the resulting package in any way, it only affects how the
test is run.
result/bin/strip-nondeterminism: bad interpreter: /nix/store/mym5b5zbzgny17ixqr8kgwmndc3k4y2r-perl-5.36.0/bin/perl -I/nix/store/mym5b5zbzgny17ixqr8kgwmndc3k4y2r-perl-5.36.0/lib: exec format error
checkInputs used to be added to nativeBuildInputs. Now we have
nativeCheckInputs to do that instead. Doing this treewide change allows
to keep hashes identical to before the introduction of
nativeCheckInputs.
Peder Bergebakken Sundt