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Build dialign2 on OSX #51262

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Build dialign2 on OSX #51262

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14 changes: 13 additions & 1 deletion recipes/dialign2/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,23 @@ mkdir -p ${PREFIX}/bin
mkdir -p ${PREFIX}/share
mkdir -p ${PREFIX}/share/dialign2

export INCLUDE_PATH="${PREFIX}/include"
export LIBRARY_PATH="${PREFIX}/lib"
export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"

if [[ `uname` == "Darwin" ]]; then
export CFLAGS="${CFLAGS} -Wno-implicit-int -Wno-implicit-function-declaration"
else
export CFLAGS="${CFLAGS}"
fi

cd src

sed -i.bak "s|strcpy ( dialign_dir , \"DIALIGN2_DIR\" );|strcpy ( par_dir , \""${PREFIX}"/share/dialign2\" );|g" dialign.c
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⚠️ Potential issue

Good improvement for installation flexibility, but watch out for quoting.

The use of ${PREFIX} in the sed command allows for a more flexible installation path, which is good practice and aligns with conda build conventions.

However, the static analysis tool flagged a potential issue with quoting. The surrounding quotes are actually unquoting the inner quotes, which may lead to unexpected behavior. To fix this, you can escape the inner quotes:

-sed -i.bak "s|strcpy ( dialign_dir , \"DIALIGN2_DIR\" );|strcpy ( par_dir , \""${PREFIX}"/share/dialign2\" );|g" dialign.c
+sed -i.bak "s|strcpy ( dialign_dir , \"DIALIGN2_DIR\" );|strcpy ( par_dir , \"${PREFIX}/share/dialign2\" );|g" dialign.c
📝 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
sed -i.bak "s|strcpy ( dialign_dir , \"DIALIGN2_DIR\" );|strcpy ( par_dir , \""${PREFIX}"/share/dialign2\" );|g" dialign.c
sed -i.bak "s|strcpy ( dialign_dir , \"DIALIGN2_DIR\" );|strcpy ( par_dir , \"${PREFIX}/share/dialign2\" );|g" dialign.c
🧰 Tools
🪛 Shellcheck

[warning] 20-20: The surrounding quotes actually unquote this. Remove or escape them.

(SC2027)

rm -rf *.bak

make CC="${CC}"
make CC="${CC}" CFLAGS="${CFLAGS}" -j"${CPU_COUNT}"
chmod 0755 dialign2-2
mv dialign2-2 ${PREFIX}/bin/dialign2-2

cd ../dialign2_dir
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19 changes: 11 additions & 8 deletions recipes/dialign2/meta.yaml
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Expand Up @@ -6,14 +6,15 @@ package:
version: {{ version }}

source:
url: http://dialign.gobics.de/download/dialign_package.tgz
url: https://dialign.gobics.de/download/dialign_package.tgz
sha256: {{ sha256 }}
patches:
- patches/patchdialign.txt

build:
number: 7
skip: True # [osx]
number: 8
run_exports:
- {{ pin_subpackage('dialign2', max_pin="x") }}

requirements:
build:
Expand All @@ -22,14 +23,16 @@ requirements:

test:
commands:
- dialign2-2 |grep usage
- dialign2-2 | grep "usage"

about:
home: http://dialign.gobics.de
home: "https://dialign.gobics.de"
license: LGPL
license_file: license/LICENSE.TXT
summary: DIALIGN multiple sequence alignment using various sources of external information
license_file: "license/LICENSE.TXT"
summary: "DIALIGN multiple sequence alignment using various sources of external information."
doc_url: "https://dialign.gobics.de"

extra:
identifiers:
- DOI:10.1093/nar/gkt283
- doi:10.1093/nar/gkt283
- biotools:dialign
4 changes: 2 additions & 2 deletions recipes/dialign2/patches/patchdialign.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
--- dialign_package/src/dialign.c 2005-02-21 17:32:55.000000000 +0100
+++ dialign_package/src/dialign.c 2018-07-26 16:46:41.962909610 +0200
--- a/src/dialign.c 2005-02-21 17:32:55.000000000 +0100
+++ b/src/dialign.c 2018-07-26 16:46:41.962909610 +0200
@@ -294,16 +294,16 @@

strcpy ( dialign_dir , "DIALIGN2_DIR" );
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