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bio-bigfile: init 1.07
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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
- e027a5d8368a053e231 : packaging kent header
- 2b2c6f4c287c6107acb : enabling patches in kent
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Add patch to tests that fixes compat with Getopt-Long-Description 0.106
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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.
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Fix pointer casts to 32-bit integers.
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[staging-next] perlPackages.MouseXGetopt: add patch
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Adds patch to test suite to make it compatible with
Getopt-Long-Descriptive >= 0.106
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Co-authored-by: Stig <git@stig.io>
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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.
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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`.
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perlPackages.SDL: fix on perl >= 5.38.0
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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.
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...into staging-next
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https://salsa.debian.org/reproducible-builds/strip-nondeterminism/-/blob/master/lib/File/StripNondeterminism/handlers/zip.pm#L29
it was working on linux because the tests are run on linux
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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.
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encrypted passwords in tests
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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
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strip-nondeterminism: fix build
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Fixes build.
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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.
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https://salsa.debian.org/reproducible-builds/strip-nondeterminism/-/tags/1.13.0
move shortenPerlShebang to postBuild to fix tests
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if theres a source $stdenv then this is needed
for structuredAttrs
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Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions. These are no longer maintained but needed for Ensembl-VEP (annotation
for genomics).
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
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