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Update Cloudspades #51456

Merged
merged 34 commits into from
Oct 18, 2024
Merged

Update Cloudspades #51456

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6da07a5
add cloudspades
pdimens Oct 15, 2024
9c352db
Rename recipes/spades/cloudspades/meta.yaml to recipes/cloudspades/me…
pdimens Oct 15, 2024
a75105d
rm flags, better versioning, rm arm
pdimens Oct 15, 2024
3fd1c6b
Merge branch 'master' into cloudspades
pdimens Oct 15, 2024
0745483
rm aarch
pdimens Oct 15, 2024
ac115e9
fix build
pdimens Oct 15, 2024
8e74a52
add ignore exports, link to the license file directly
pdimens Oct 15, 2024
b548ac9
fix constraint
pdimens Oct 15, 2024
2045d43
fix license path
pdimens Oct 15, 2024
e8c704e
simplify tests b/c cloudspades acts different
pdimens Oct 15, 2024
ad59ff4
Merge branch 'master' into cloudspades
pdimens Oct 15, 2024
3d88e6f
skip osk. make life easier
pdimens Oct 15, 2024
57b00e9
add proper test
pdimens Oct 15, 2024
4f2d95b
add gz
pdimens Oct 15, 2024
6692969
try building with less threads
mencian Oct 16, 2024
9260860
fix tests
mencian Oct 16, 2024
0399e25
edit test command
mencian Oct 16, 2024
a373b6b
do not build on aarch64/arm64
mencian Oct 16, 2024
817a88b
Merge branch 'master' into cloudspades
mencian Oct 16, 2024
af16fd4
add case for Darwin
mencian Oct 16, 2024
871a400
Merge branch 'master' into cloudspades
mencian Oct 16, 2024
140ff1c
Merge branch 'master' into cloudspades
mencian Oct 16, 2024
f1a7429
edit case
mencian Oct 16, 2024
a443735
Merge branch 'master' into cloudspades
mencian Oct 16, 2024
73936dd
Add "-D_LIBCPP_DISABLE_AVAILABILITY" for OSX
martin-g Oct 16, 2024
083460a
skip osx x86_64 for now
mencian Oct 16, 2024
8c63287
Merge branch 'bioconda:master' into cloudspades
pdimens Oct 17, 2024
f8eb7e7
simplify build script, move things manually, add real test
pdimens Oct 17, 2024
3dcbd08
Merge branch 'master' into cloudspades
pdimens Oct 17, 2024
718787e
fix mv command
pdimens Oct 17, 2024
17d00b4
bump build number
pdimens Oct 17, 2024
2a74765
rm the mv statement, it's redundant
pdimens Oct 17, 2024
7b011b2
rm the test?
pdimens Oct 17, 2024
3913272
rm arm
pdimens Oct 18, 2024
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11 changes: 6 additions & 5 deletions recipes/cloudspades/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@

set -e -o pipefail -x

export LIBRARY_PATH="${PREFIX}/lib"
export INCLUDE_PATH="${PREFIX}/include"
export CFLAGS="${CFLAGS} -O3 -fcommon"
export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY -fsigned-char"
#export LIBRARY_PATH="${PREFIX}/lib"
#export INCLUDE_PATH="${PREFIX}/include"
#export CFLAGS="${CFLAGS} -O3 -fcommon"
#export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY"

case $(uname) in
Linux)
Expand All @@ -16,5 +16,6 @@ case $(uname) in
;;
esac

mkdir -p ${PREFIX}/bin ${PREFIX}/share
cd assembler
PREFIX="${PREFIX}" bash spades_compile.sh "${THREADS}" -DSPADES_ENABLE_PROJECTS="all"
./spades_compile.sh "${THREADS}"
4 changes: 1 addition & 3 deletions recipes/cloudspades/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ source:
sha256: {{ sha256 }}

build:
number: 1
number: 2
skip: True # [osx]
run_exports:
- {{ pin_subpackage('cloudspades', max_pin="x") }}
Expand Down Expand Up @@ -50,7 +50,5 @@ about:
doc_url: "https://github.com/ablab/spades/tree/cloudspades-ismb"

extra:
additional-platforms:
- linux-aarch64
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What was the problem with aarch64 here ?

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It fails to compile on ARM

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I guess it failed to compile due to the usage of signed chars.
The support has been removed with this PR - https://github.com/bioconda/bioconda-recipes/pull/51456/files#diff-be671f9588fb1b742546ddcfd20773418719432b8e42799df8df52a9e7a3df9eL8 (-fsigned-char is gone)

What is the correct way to pass CXXFLAGS for this recipe ?

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@pdimens pdimens Oct 21, 2024 •
edited
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It seems to work correctly without any flags but the previous commits that borrowed the CXX flags from the regular spades recipe built, however the resulting installation had errors when running (same for the current spades recipe, which remains unresolved). AFAIK, there isn't an example of a proper spades ARM build on bioconda and the existing spades (regular) build is currently bugged and unresolved. See #51390

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I know just about nothing about compilation, so I'm able to identify that there is an issue, but powerless to implement meaningful fixes.

recipe-maintainers:
- pdimens