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Update libmaus2 to v2.0.183 #52154

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merged 11 commits into from
Nov 18, 2024
Merged

Update libmaus2 to v2.0.183 #52154

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2fbd5e0
Update libmaus2 to v2.0.183
mencian Nov 18, 2024
7187fb0
Update meta.yaml
mencian Nov 18, 2024
d8f3d46
Update build.sh
mencian Nov 18, 2024
98c789a
Update build.sh
mencian Nov 18, 2024
8edf93d
Update meta.yaml
mencian Nov 18, 2024
1deb425
Update build.sh
mencian Nov 18, 2024
1d0b928
Update meta.yaml
mencian Nov 18, 2024
8c2052c
Update build.sh
mencian Nov 18, 2024
7f9c3c4
Update meta.yaml
mencian Nov 18, 2024
219165f
clean up recipe
mencian Nov 18, 2024
dca0f25
try large aarch64 machine
mencian Nov 18, 2024
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14 changes: 11 additions & 3 deletions recipes/libmaus2/build.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,18 @@
#!/bin/bash
set -eu
export LIBS="-lstdc++fs -lcurl"
export LIBS="-lstdc++ -lcurl -lz -ldeflate"

./configure --prefix $PREFIX --with-snappy --with-io_lib
autoreconf -if
autoupdate
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🛠️ Refactor suggestion

Add error handling for autotools commands

The autoreconf and autoupdate commands might fail silently. Consider adding error checking:

-autoreconf -if
-autoupdate
+if ! autoreconf -if; then
+  echo "Failed to run autoreconf"
+  exit 1
+fi
+if ! autoupdate; then
+  echo "Failed to run autoupdate"
+  exit 1
+fi
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
autoreconf -if
autoupdate
if ! autoreconf -if; then
echo "Failed to run autoreconf"
exit 1
fi
if ! autoupdate; then
echo "Failed to run autoupdate"
exit 1
fi

./configure --prefix="${PREFIX}" CXX="${CXX}" CC="${CC}" \
CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY"
LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
--with-snappy --with-io_lib --with-libdeflate \
--with-libsecrecy --with-nettle \
--with-lzma --with-gmp

cat config.log

make -j${CPU_COUNT}
make -j"${CPU_COUNT}"
make install
Comment on lines +13 to 14
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🛠️ Refactor suggestion

Add error handling for make commands

Consider adding error handling and logging for make commands:

-make -j"${CPU_COUNT}"
-make install
+if ! make -j"${CPU_COUNT}"; then
+  echo "Build failed. Last 50 lines of config.log:"
+  tail -n 50 config.log
+  exit 1
+fi
+if ! make install; then
+  echo "Installation failed"
+  exit 1
+fi
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
make -j"${CPU_COUNT}"
make install
if ! make -j"${CPU_COUNT}"; then
echo "Build failed. Last 50 lines of config.log:"
tail -n 50 config.log
exit 1
fi
if ! make install; then
echo "Installation failed"
exit 1
fi

42 changes: 25 additions & 17 deletions recipes/libmaus2/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{% set name = "libmaus2" %}
{% set version = "2.0.810" %}
{% set datestamp = "20220216151520" %}
{% set sha256hash = "6639289aba6bbece3057ab7d1782a1b94b80a9ae22fc3d136a78ba8f7b9edaee" %}
{% set version = "2.0.813" %}
{% set datestamp = "20221210220409" %}
{% set sha256 = "4125f8daefd6900185675026498369457088e25e81029597659249be49cd5261" %}

package:
name: {{ name }}
Expand All @@ -10,47 +10,55 @@ package:
build:
# There's some issue with clang
skip: True # [osx]
number: 6
number: 0
run_exports:
- {{ pin_subpackage('libmaus2', max_pin='x.x') }}
- {{ pin_subpackage('libmaus2', max_pin='x') }}

source:
url: https://gitlab.com/german.tischler/libmaus2/-/archive/{{ version }}-release-{{ datestamp }}/libmaus2-{{ version }}-release-{{ datestamp }}.tar.gz
sha256: {{ sha256hash }}
patches:
sha256: {{ sha256 }}
#patches:
# Until gcc >=8 is being used
- patch
#- patch

requirements:
build:
- make
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- autoconf
- automake
- libtool
- pkg-config
host:
- boost-cpp
- libcurl
# snappy 1.1.9 introduced a binary incompatible build change (https://github.com/mhx/dwarfs/issues/56#issuecomment-896857211)
# enabling -fno-rtti. libmaus needs typeid, which is only available with activated rtti.
# Hence, we stick with snappy 1.1.8
- snappy =1.1.8
- snappy =1.1.8
- staden_io_lib >=1.14.14
- libdeflate
- gmp
- nettle
- zlib
run:
- boost-cpp
- libcurl
- snappy =1.1.8
- staden_io_lib >=1.14.14
ignore_run_exports:
- snappy

about:
home: https://gitlab.com/german.tischler/libmaus2
license: GPL3
summary: collection of data structures and algorithms for NGS data

test:
commands:
- echo

about:
home: https://gitlab.com/german.tischler/libmaus2
license: GPL-3.0-or-later
license_family: GPL3
license_file: GPLv3
summary: "Collection of data structures and algorithms for NGS data."
dev_url: https://gitlab.com/german.tischler/libmaus2

extra:
additional-platforms:
- linux-aarch64
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