-
Notifications
You must be signed in to change notification settings - Fork 3.3k
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Update svdss to 2.0.0 #51519
Update svdss to 2.0.0 #51519
Changes from 4 commits
File filter
Filter by extension
Conversations
Jump to
Diff view
Diff view
There are no files selected for viewing
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,10 +1,24 @@ | ||
#!/usr/bin/env bash | ||
|
||
mkdir -p build | ||
cd build | ||
cmake -DCMAKE_BUILD_TYPE=Release -DCONDAPREFIX=${PREFIX} .. | ||
make | ||
cd .. | ||
#!/bin/bash | ||
|
||
mkdir -p ${PREFIX}/bin | ||
cp SVDSS ${PREFIX}/bin | ||
export INCLUDE_PATH="${PREFIX}/include" | ||
export LIBRARY_PATH="${PREFIX}/lib" | ||
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | ||
export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" | ||
export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" | ||
|
||
if [[ `uname` == "Darwin" ]]; then | ||
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" | ||
else | ||
export CONFIG_ARGS="" | ||
fi | ||
|
||
cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \ | ||
-DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \ | ||
-DCMAKE_C_FLAGS="${CFLAGS}" \ | ||
"${CONFIG_ARGS}" | ||
cmake --build build -j "${CPU_COUNT}" -v | ||
|
||
chmod 0755 SVDSS | ||
cp -f SVDSS ${PREFIX}/bin |
This file was deleted.
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,5 +1,5 @@ | ||
{% set version = "1.0.5" %} | ||
{% set sha256 = "98345630451e98a43af9c807c9cf739cce58f6582d860ceb5daa00bdb50950df" %} | ||
{% set version = "2.0.0" %} | ||
{% set sha256 = "825324dbdd70474b2a527925a25dea94b597ef579dee117645f285d678985652" %} | ||
|
||
package: | ||
name: svdss | ||
|
@@ -10,8 +10,10 @@ source: | |
sha256: {{ sha256 }} | ||
|
||
build: | ||
number: 3 | ||
skip: True # [osx] | ||
number: 0 | ||
#skip: True # [osx] | ||
run_exports: | ||
- {{ pin_subpackage('svdss', max_pin="x") }} | ||
|
||
requirements: | ||
build: | ||
|
@@ -20,16 +22,20 @@ requirements: | |
- make | ||
- automake | ||
- autoconf | ||
- coreutils | ||
- cmake >=3.14 | ||
- libtool | ||
- cmake | ||
- git | ||
host: | ||
- libgomp # [linux] | ||
- llvm-openmp # [osx] | ||
- htslib | ||
- gsl | ||
- zlib | ||
- bzip2 | ||
- xz | ||
run: | ||
- libgomp # [linux] | ||
- llvm-openmp # [osx] | ||
- samtools >=1.9 | ||
- bcftools >=1.9 | ||
|
||
|
@@ -38,12 +44,17 @@ test: | |
- SVDSS --version | ||
|
||
about: | ||
home: https://github.com/Parsoa/SVDSS | ||
home: "https://github.com/Parsoa/SVDSS" | ||
license: MIT | ||
summary: Structural Variant Discovery from Sample-specific Strings | ||
license_family: MIT | ||
license_file: LICENSE | ||
summary: "Structural Variant Discovery from Sample-specific Strings." | ||
dev_url: "https://github.com/Parsoa/SVDSS" | ||
doc_url: "https://github.com/Parsoa/SVDSS/blob/v{{ version }}/README.md" | ||
|
||
extra: | ||
identifiers: | ||
- biotools:svdss | ||
- doi:10.1038/s41592-022-01674-1 | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 💡 Codebase verification DOI does not resolve correctly The DOI 🔗 Analysis chainDOI addition is excellent. The inclusion of a DOI (Digital Object Identifier) is a valuable addition for academic citation and tracking of the software. Please run the following script to verify the DOI: The previous script did not verify the DOI as intended. Please run the following script to verify the DOI: 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Verify the DOI
# Extract the DOI
doi=$(grep -oP 'doi:\K[^\s]+' recipes/svdss/meta.yaml)
# Check if the DOI resolves
if curl -s -o /dev/null -w "%{http_code}" "https://doi.org/$doi" | grep -q "200"; then
echo "DOI $doi is valid and resolves correctly."
else
echo "Error: DOI $doi does not resolve. Please check the DOI."
fi
Length of output: 2219 Script: #!/bin/bash
# Description: Verify the DOI
# Extract the DOI
doi=$(grep -oP 'doi:\K[^\s]+' recipes/svdss/meta.yaml)
# Check if the DOI resolves
if curl -s -o /dev/null -w "%{http_code}" "https://doi.org/$doi" | grep -q "200"; then
echo "DOI $doi is valid and resolves correctly."
else
echo "Error: DOI $doi does not resolve. Please check the DOI."
fi
Length of output: 346 |
||
recipe-maintainers: | ||
- ldenti |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
💡 Codebase verification
macOS support may not be fully enabled.
skip
directive for macOS has been commented out.llvm-openmp
are still present inmeta.yaml
(lines 30 and 38).build-osx.sh
) found.Please review and ensure that all macOS support configurations are correctly implemented.
🔗 Analysis chain
Build section changes look good, but verify macOS support.
The build number has been correctly reset to 0 for the new version. The addition of the
run_exports
section is a good practice for ensuring correct version pinning.The macOS skip directive has been commented out. Please confirm that the package now supports macOS by running the following script:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
Length of output: 864
Script:
Length of output: 717