statically link against conda htslib instead of bundled htslib - #4

Draft

aryarm wants to merge 25 commits into

mainfrom

Commits on Mar 17, 2026

create devcontainer for compiling on the fly
aryarm
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806d74a
oops fix typo in htslib
aryarm
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40608d4
ignore object files after compilation
aryarm
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c1e37f9
include cstdint in region permanently
aryarm
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042251a
ensure binary in artifacts is static
aryarm
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3578e4c
also skip builds on windows
aryarm
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4c5bf07
retry to build static in ci
aryarm
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4a16f3d
allow overriding from bioconda.yml
aryarm
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515dabe
rm static attempt
aryarm
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ed23612
use linked instead of bundled htslib
aryarm
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a09c294
also patch DenovoFinder and PhasingChecker
aryarm
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1d7a6e7
fix 0002 patch
aryarm
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2f15766
try to fix patch again
aryarm
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cb927a0
try to fix 0002 patch yet again
aryarm
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d808568

Commits on Mar 18, 2026

Commits on Mar 19, 2026

Update LDFLAGS to include additional libraries when building static
aryarm
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a955a01
rm quotes around static arg
aryarm
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c05b3c4
use jinja2 templating for static build
aryarm
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e3d477f

Commits on Mar 20, 2026

try static jinja2 templating again
aryarm
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1e68c7f
also test if the static build is truly static
aryarm
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fd7e219

Commits on Mar 23, 2026

ensure sed is properly patching the recipe
aryarm
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bea901e
retry with static of 0 and 1
aryarm
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b06c58a