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Update FINEMAP to 1.4.2 #51978
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Update FINEMAP to 1.4.2 #51978
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c86a4c6
bump/finemap
aryarm 915d4f3
add run_exports to FINEMAP recipe
aryarm ed0ade2
add script and build info
aryarm 8a0e784
include compiler since this package is not noarch
aryarm f6e4b07
only build on linux
aryarm f9bee23
add outline for osx
aryarm 21fac97
add suggestions from PR review
aryarm f6d3bca
skip building finemap if not linux64
aryarm 7519e0b
add license file and use noarch generic now
aryarm f1c75d6
completely give up on osx
aryarm 1696b58
remove noarch generic
aryarm 83fc1dc
skip noarch generic lint
aryarm acc89b4
add required dependencies, use LICENSE from source, and use example d…
aryarm 41777dd
skip more lint checks
aryarm 7b89b06
Merge branch 'master' into patch-1
richard-burhans e610d61
move build requirements to host and whitelist
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Original file line number | Diff line number | Diff line change |
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@@ -1,37 +1,65 @@ | ||
# This file created by conda-build 3.22.0 | ||
# meta.yaml template originally from: | ||
# /home/conda/conda-forge/recipes/finemap, last modified Thu Oct 20 22:53:08 2022 | ||
# ------------------------------------------------ | ||
{% set name = "finemap" %} | ||
{% set version = "1.4.2" %} | ||
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||
package: | ||
name: finemap | ||
version: 1.4.1 | ||
name: {{ name }} | ||
version: {{ version }} | ||
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source: | ||
sha256: 75c919d9cc981bc08e1a982b1632110109ffe6a057e803c9aa36c143aa56d546 | ||
url: http://www.christianbenner.com/finemap_v1.4.1_x86_64.tgz | ||
- url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz | ||
sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 | ||
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||
build: | ||
binary_relocation: false | ||
noarch: generic | ||
number: '0' | ||
number: 0 | ||
# skip osx since binary cannot be relinked b/c it was built without the -headerpad_max_install_names option | ||
skip: True # [not linux64] | ||
run_exports: | ||
- {{ pin_subpackage('finemap', max_pin="x") }} | ||
script: | ||
- install -Dd ${PREFIX}/bin | ||
- install -D -m 755 finemap_v1.4.1_x86_64 ${PREFIX}/bin/finemap | ||
string: '0' | ||
- mkdir -p ${PREFIX}/bin | ||
- install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap | ||
missing_dso_whitelist: | ||
- /lib64/libdl.so.2 | ||
- /lib64/libm.so.6 | ||
- $RPATH/libgomp.so.1 | ||
- /lib64/libgcc_s.so.1 | ||
- /lib64/libpthread.so.0 | ||
- /lib64/libc.so.6 | ||
- /lib64/ld-linux-x86-64.so.2 | ||
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||
requirements: | ||
build: [] | ||
host: [] | ||
run: [] | ||
host: | ||
- {{ stdlib("c") }} | ||
- libgomp | ||
- libgcc | ||
run: | ||
- {{ stdlib("c") }} | ||
- libgomp | ||
- libgcc | ||
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||
test: | ||
source_files: | ||
- example | ||
commands: | ||
- test -f $PREFIX/bin/finemap | ||
- finemap --help | ||
- finemap --sss --in-files example/data | ||
- finemap --cond --in-files example/data | ||
- finemap --config --in-files example/data --rsids rs30,rs11 | ||
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||
about: | ||
home: http://www.christianbenner.com | ||
license: Other | ||
license: Custom Academic | ||
license_url: http://www.christianbenner.com/license_finemap_v1.4.html | ||
# use LICENSE file in downloaded source | ||
license_file: LICENSE | ||
summary: Program for identifying causal SNPs and their effect sizes and heritability | ||
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|
||
contributions | ||
summary: > | ||
Program for identifying causal SNPs and their effect sizes and heritability contributions | ||
|
||
extra: | ||
copy_test_source_files: true | ||
final: true | ||
skip-lints: | ||
- should_use_compilers | ||
- should_be_noarch_generic | ||
- version_constraints_missing_whitespace | ||
recipe-maintainers: | ||
- aryarm | ||
- danielnachun |
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please use the
compiler
directive here.There was a problem hiding this comment.
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Hi @bgruening !
Is this what you're thinking?
I actually had something like this in 8a0e784, but we decided to remove it in #51978 (comment), since I'm simply copying a binary and not compiling it. Shall I add it back?
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Yes this is what I was thinking. If @martin-g is ok with the way you have it now let's keep it.
Adding libgomp and libgcc will be done by the complier directive and it's a bit more portable. But you eitherway skip everything but linux64. So 🤷
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Ok, thanks for explaining!
I would like to make it work on macos eventually, so maybe it's a good idea to go with the more portable option for better future proofing. Or I can add a comment that explains to do that in the future.
I'll wait to hear thoughts from @martin-g
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I'll take a closer look later today!
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Do you need anything in the
requirements > build
section if you don't build it from source ?There was a problem hiding this comment.
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I tried that locally. The tests still seem to pass when I remove the
requirements > build
section, butconda-bld
will issue a bunch of warnings.Should I just ignore those by adding the DSOs to
missing_dso_whitelist
? I was concerned that adding a package tomissing_dso_whitelist
might preventconda-bld
from automatically updating the path to the DSO in the binary (using patchelf) - since I couldn't find much info about the exact function ofmissing_dso_whitelist
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I don't have any experience with this kind of problems but I think you need to move those deps to
requirements > host
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That makes sense. From what I've read online, shared libraries like those are supposed to be placed in the host section to ensure portability.
But when I move those requirements into the host section, I still get the same warnings mentioned above. So I guess I'll add them to
missing_dso_whitelist
Also please feel free to let me know if there's somewhere else where I should also try to ask these questions. I've only recently been trying to learn how to create conda recipes, so I'm not very familiar with all of the resources yet.