Rebuild Augustus recipe #51641
Rebuild Augustus recipe #51641
Conversation
|
Warning Rate limit exceeded@mencian has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 3 minutes and 1 seconds before requesting another review. ⌛ How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. 🚦 How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our FAQ for further information. 📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces several modifications across three main files related to the Augustus software package. In Possibly related PRs
Suggested labels
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (2)
recipes/augustus/build.sh (2)
14-18: LGTM! Consider making the else clause more explicit.The conditional check is well-structured and the SQLite configuration is properly documented with a reference to the Boost issue.
Consider making the else clause more explicit:
if [[ "$(uname)" = Darwin ]]; then # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501 sqlite= else - sqlite='SQLITE=true' + # Enable SQLite for non-Darwin platforms + sqlite='SQLITE=true' fi
46-46: LGTM! Consider documenting the Build.PL purpose.While the force copy is appropriate, it would be helpful to document why Build.PL needs to be copied from the recipe directory.
Add a comment explaining the purpose:
+# Copy custom Build.PL file that defines the perl module build configuration cp -f ${RECIPE_DIR}/Build.PL ./
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- recipes/augustus/build.sh (2 hunks)
- recipes/augustus/meta.yaml (2 hunks)
- recipes/augustus/patches/0001-Makefile.patch (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/augustus/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (8)
recipes/augustus/patches/0001-Makefile.patch (2)
9-13: LGTM! Installation path variables follow best practices.The changes properly implement GNU Make installation directory conventions:
- Using
DESTDIRfor staging installations- Making
prefixconfigurable with fallback toPREFIX- Correctly constructing
bindir
16-21: Good improvement using CURDIR instead of PWD.The change from
PWDtoCURDIRis more reliable as it's a Make-specific variable that's guaranteed to work consistently across different shell environments.recipes/augustus/build.sh (2)
21-32: LGTM! Build configuration follows best practices.The make command is well-structured with:
- Proper use of compiler variables
- Consistent PREFIX usage
- Efficient parallel builds
5-8: Consider the implications of aggressive optimization and variable redundancy.
- The
-O3flag enables aggressive optimization which might lead to unexpected behavior. Consider using-O2for a better balance between performance and stability.INCLUDESandLIBPATHappear redundant withCXXFLAGSandLDFLAGS. Consider consolidating these to reduce complexity.Let's verify if Augustus has any known issues with -O3:
recipes/augustus/meta.yaml (4)
1-7: LGTM! Good use of Jinja2 templating.The introduction of variables for name, version, and sha256 improves maintainability. The package metadata is properly structured.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
18-20: LGTM! Good addition of run_exports for ABI compatibility.The
run_exportssection withmax_pin="x"ensures that downstream packages will maintain compatibility within the same major version, preventing ABI breakage. This aligns well with the PR objectives.
157-167: LGTM! Enhanced metadata with secure URLs and documentation links.Good improvements:
- Updated to HTTPS for security
- Added links to source code and version-specific documentation
174-174: LGTM! Added Galaxy training identifier.The addition of
usegalaxy-eu:augustus_trainingenhances discoverability for Galaxy workflow users.
| INSTALLDIR = /opt/augustus-$(AUGVERSION) | ||
|
|
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider making INSTALLDIR configurable.
The hardcoded /opt path in INSTALLDIR might cause issues in containerized or managed environments. Consider making it respect the prefix:
-INSTALLDIR = /opt/augustus-$(AUGVERSION)
+INSTALLDIR = $(prefix)/share/augustus-$(AUGVERSION)This would better align with standard Unix filesystem hierarchy and package management practices.
📝 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.
| INSTALLDIR = /opt/augustus-$(AUGVERSION) | |
| INSTALLDIR = $(prefix)/share/augustus-$(AUGVERSION) | |
| - ln -sf $(INSTALLDIR)/bin/augustus $(PREFIX)/bin/augustus | ||
| - ln -sf $(INSTALLDIR)/bin/etraining $(PREFIX)/bin/etraining | ||
| - ln -sf $(INSTALLDIR)/bin/prepareAlign $(PREFIX)/bin/prepareAlign | ||
| - ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(PREFIX)/bin/fastBlockSearch | ||
| - if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(PREFIX)/bin/load2db ; fi | ||
| - if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(PREFIX)/bin/getSeq ; fi | ||
| + ln -sf $(INSTALLDIR)/bin/augustus $(bindir)/augustus | ||
| + ln -sf $(INSTALLDIR)/bin/etraining $(bindir)/etraining | ||
| + ln -sf $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign | ||
| + ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearch | ||
| + if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi | ||
| + if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fi |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider using install command for symlinks.
While the symlink creation works, using the install command would be more idiomatic and provide better error handling:
- ln -sf $(INSTALLDIR)/bin/augustus $(bindir)/augustus
- ln -sf $(INSTALLDIR)/bin/etraining $(bindir)/etraining
- ln -sf $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign
- ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearch
+ install -d $(bindir)
+ install -m 755 -s $(INSTALLDIR)/bin/augustus $(bindir)/augustus
+ install -m 755 -s $(INSTALLDIR)/bin/etraining $(bindir)/etraining
+ install -m 755 -s $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign
+ install -m 755 -s $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearchFor the conditional installations:
- if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi
- if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fi
+ if [ -f $(INSTALLDIR)/bin/load2db ] ; then install -m 755 -s $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi
+ if [ -f $(INSTALLDIR)/bin/getSeq ] ; then install -m 755 -s $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fiThis approach:
- Ensures the target directory exists
- Sets proper permissions
- Strips debugging symbols (-s flag)
- Provides better error handling
📝 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.
| - ln -sf $(INSTALLDIR)/bin/augustus $(PREFIX)/bin/augustus | |
| - ln -sf $(INSTALLDIR)/bin/etraining $(PREFIX)/bin/etraining | |
| - ln -sf $(INSTALLDIR)/bin/prepareAlign $(PREFIX)/bin/prepareAlign | |
| - ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(PREFIX)/bin/fastBlockSearch | |
| - if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(PREFIX)/bin/load2db ; fi | |
| - if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(PREFIX)/bin/getSeq ; fi | |
| + ln -sf $(INSTALLDIR)/bin/augustus $(bindir)/augustus | |
| + ln -sf $(INSTALLDIR)/bin/etraining $(bindir)/etraining | |
| + ln -sf $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign | |
| + ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearch | |
| + if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi | |
| + if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fi | |
| install -d $(bindir) | |
| install -m 755 -s $(INSTALLDIR)/bin/augustus $(bindir)/augustus | |
| install -m 755 -s $(INSTALLDIR)/bin/etraining $(bindir)/etraining | |
| install -m 755 -s $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign | |
| install -m 755 -s $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearch | |
| if [ -f $(INSTALLDIR)/bin/load2db ] ; then install -m 755 -s $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi | |
| if [ -f $(INSTALLDIR)/bin/getSeq ] ; then install -m 755 -s $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fi |
| # Fix perl shebang | ||
| sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl | ||
| rm -rf ${SRC_DIR}/scripts/*.bak |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add error checking for Perl script modifications.
While the shebang fix is good, the operation could fail silently if no .pl files exist.
Consider adding error checking:
-sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl
-rm -rf ${SRC_DIR}/scripts/*.bak
+# Check if Perl scripts exist
+if ls ${SRC_DIR}/scripts/*.pl >/dev/null 2>&1; then
+ sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl
+ rm -rf ${SRC_DIR}/scripts/*.bak
+else
+ echo "Warning: No Perl scripts found in ${SRC_DIR}/scripts/"
+fi📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # Fix perl shebang | |
| sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl | |
| rm -rf ${SRC_DIR}/scripts/*.bak | |
| # Fix perl shebang | |
| # Check if Perl scripts exist | |
| if ls ${SRC_DIR}/scripts/*.pl >/dev/null 2>&1; then | |
| sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl | |
| rm -rf ${SRC_DIR}/scripts/*.bak | |
| else | |
| echo "Warning: No Perl scripts found in ${SRC_DIR}/scripts/" | |
| fi |
| - {{ compiler('cxx') }} | ||
| host: | ||
| - zlib | ||
| - samtools ==0.1.19 | ||
| - samtools |
There was a problem hiding this comment.
💡 Codebase verification
Samtools version constraint removal requires attention
The codebase history shows that Augustus previously required samtools version 0.1.19 specifically. The build logs indicate direct integration with samtools through include paths and linking. Removing this strict version requirement could be problematic since:
- Augustus has direct dependencies on samtools header files and libraries
- The package previously used a very old version (0.1.19) of samtools
- Newer versions of samtools may have incompatible API changes
Please:
- Restore the version constraint to
samtools ==0.1.19 - Or verify compatibility with newer samtools versions by testing the build process
🔗 Analysis chain
Verify samtools compatibility after removing version constraint.
The version constraint for samtools has been removed. While this provides more flexibility, please ensure that the package is compatible with recent samtools versions to prevent potential runtime issues.
Let me gather more information about the augustus package and its relationship with samtools.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are any known compatibility issues with samtools in the codebase
rg -i "samtools" . --type cpp --type c --type perl -C 2
Length of output: 438
Script:
#!/bin/bash
# Check augustus source code and build files for samtools usage
rg -i "samtools" ./recipes/augustus --type yaml --type txt -C 3
# Check test files for samtools usage patterns
fd "test" ./recipes/augustus -t f -x rg -i "samtools" {} -C 2 \;
# Check if there are any version constraints in previous versions
git log -p ./recipes/augustus/meta.yaml | rg -i "samtools"
Length of output: 1906
There was a problem hiding this comment.
Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (1)
recipes/augustus/build.sh (1)
15-19: Make the else clause more explicit.While the Darwin-specific handling is well documented, the else clause could be more explicit about which platforms will enable SQLite.
if [[ "$(uname)" = Darwin ]]; then # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501 sqlite= else - sqlite='SQLITE=true' + # Enable SQLite for non-Darwin platforms + sqlite='SQLITE=true' fi
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- recipes/augustus/build.sh (3 hunks)
- recipes/augustus/patches/0001-Makefile.patch (1 hunks)
- recipes/augustus/patches/utrrnaseq.patch (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/augustus/patches/0001-Makefile.patch
🔇 Additional comments (3)
recipes/augustus/patches/utrrnaseq.patch (1)
9-10: Verify the impact of optimization level change.Changing from
-O0to-O3significantly alters the optimization level from none to maximum. While this generally improves performance, it can potentially affect numerical precision or behavior in scientific computing applications.Consider testing the output consistency between
-O0and-O3builds, especially for floating-point calculations.recipes/augustus/build.sh (2)
35-37: Previous comment about error handling for Perl scripts is still applicable.
5-8: Consider the implications of aggressive optimization.The
-O3optimization flag might cause issues in some architectures or with certain compilers. Additionally, theUSE_BOOSTflag is defined but there's no explicit check for Boost availability.Let's verify if Boost is properly declared as a dependency:
| INCLS += $(INCLUDE_PATH_BOOST) # set boost include path in INCLUDE_PATH_BOOST, if boost is not installed system-wide | ||
| LDFLAGS += $(LIBRARY_PATH_BOOST) # set boost library path in LIBRARY_PATH_BOOST, if boost is not installed system-wide | ||
|
|
||
| @@ -29,6 +29,7 @@ utrrnaseq: $(OBJS) |
There was a problem hiding this comment.
Use installation prefix variable instead of hard-coded paths.
The binary installation path is hard-coded as ../../bin/. This should use installation prefix variables for consistency with other Makefile changes mentioned in the PR, making it more flexible for different installation scenarios.
Consider this modification:
- cp -f utrrnaseq ../../bin/utrrnaseq
+ cp -f utrrnaseq $(prefix)/bin/utrrnaseq
- rm ../../bin/utrrnaseq
+ rm $(prefix)/bin/utrrnaseqAlso applies to: 22-22
| @@ -39,7 +44,7 @@ cd perl-build | |||
| # affects tests for Augustus 3.3: | |||
| # https://github.com/Gaius-Augustus/Augustus/commit/7ca3ab | |||
| #sed -i'' -e '1s/perl -w/perl/' *.pl | |||
| cp ${RECIPE_DIR}/Build.PL ./ | |||
| cp -f ${RECIPE_DIR}/Build.PL ./ | |||
There was a problem hiding this comment.
Add error checking for Build.PL copy operation.
The force flag (-f) could mask issues if the source file doesn't exist.
-cp -f ${RECIPE_DIR}/Build.PL ./
+if [ -f "${RECIPE_DIR}/Build.PL" ]; then
+ cp -f "${RECIPE_DIR}/Build.PL" ./
+else
+ echo "Error: ${RECIPE_DIR}/Build.PL not found"
+ 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.
| cp -f ${RECIPE_DIR}/Build.PL ./ | |
| if [ -f "${RECIPE_DIR}/Build.PL" ]; then | |
| cp -f "${RECIPE_DIR}/Build.PL" ./ | |
| else | |
| echo "Error: ${RECIPE_DIR}/Build.PL not found" | |
| exit 1 | |
| fi |
| make \ | ||
| CC="${CC}" \ | ||
| CXX="${CXX}" \ | ||
| INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \ | ||
| LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \ | ||
| INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \ | ||
| LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \ | ||
| INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \ | ||
| LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \ | ||
| COMPGENPRED=true \ | ||
| MYSQL=false \ | ||
| "${sqlite}" -j"${CPU_COUNT}" |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider limiting parallel build jobs.
While using ${CPU_COUNT} for parallel builds is good for performance, it might cause issues on machines with many cores due to memory constraints.
- "${sqlite}" -j"${CPU_COUNT}"
+ "${sqlite}" -j"$(( CPU_COUNT < 4 ? CPU_COUNT : 4 ))"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| make \ | |
| CC="${CC}" \ | |
| CXX="${CXX}" \ | |
| INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \ | |
| LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \ | |
| INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \ | |
| LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \ | |
| INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \ | |
| LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \ | |
| COMPGENPRED=true \ | |
| MYSQL=false \ | |
| "${sqlite}" -j"${CPU_COUNT}" | |
| make \ | |
| CC="${CC}" \ | |
| CXX="${CXX}" \ | |
| INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \ | |
| LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \ | |
| INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \ | |
| LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \ | |
| INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \ | |
| LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \ | |
| COMPGENPRED=true \ | |
| MYSQL=false \ | |
| "${sqlite}" -j"$(( CPU_COUNT < 4 ? CPU_COUNT : 4 ))" |
| chmod 0755 bin/augustus | ||
| mv bin/* $PREFIX/bin/ | ||
| mv scripts/* $PREFIX/bin/ |
There was a problem hiding this comment.
Add comprehensive permission setting and error checking.
Consider setting appropriate permissions for all executables and add error checking for move operations.
-chmod 0755 bin/augustus
-mv bin/* $PREFIX/bin/
-mv scripts/* $PREFIX/bin/
-mv config/* $PREFIX/config/
+# Set permissions for all executables
+find bin scripts -type f -executable -exec chmod 0755 {} \;
+
+# Move files with error checking
+for dir in bin scripts; do
+ if [ -d "$dir" ] && [ "$(ls -A $dir)" ]; then
+ mv $dir/* $PREFIX/bin/ || { echo "Error moving $dir contents"; exit 1; }
+ fi
+done
+
+if [ -d "config" ] && [ "$(ls -A config)" ]; then
+ mv config/* $PREFIX/config/ || { echo "Error moving config contents"; 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.
| chmod 0755 bin/augustus | |
| mv bin/* $PREFIX/bin/ | |
| mv scripts/* $PREFIX/bin/ | |
| # Set permissions for all executables | |
| find bin scripts -type f -executable -exec chmod 0755 {} \; | |
| # Move files with error checking | |
| for dir in bin scripts; do | |
| if [ -d "$dir" ] && [ "$(ls -A $dir)" ]; then | |
| mv $dir/* $PREFIX/bin/ || { echo "Error moving $dir contents"; exit 1; } | |
| fi | |
| done | |
| if [ -d "config" ] && [ "$(ls -A config)" ]; then | |
| mv config/* $PREFIX/config/ || { echo "Error moving config contents"; exit 1; } | |
| fi |
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/augustus/build.sh (2)
15-19: Document SQLite configuration rationale.While the SQLite configuration for Darwin systems references a Boost ticket, consider adding more detailed documentation about:
- The specific compilation issues on Darwin
- Whether this is still relevant for the current Boost version
if [[ "$(uname)" = Darwin ]]; then - # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501 + # SQLITE is disabled on Darwin systems due to compilation conflicts between Boost and SQLite + # Reference: https://svn.boost.org/trac10/ticket/13501 + # TODO: Verify if this is still needed with current Boost versions sqlite=
Line range hint
1-3: Add comprehensive header documentation.Consider adding a header comment block that includes:
- Script purpose and requirements
- Expected environment variables
- Dependencies that must be present
#!/bin/bash +# Build script for Augustus bioinformatics software +# Requirements: +# - Compiler with C++14 support +# - Boost libraries +# - Bamtools, LPSolve, and HTSlib development files +# - Perl 5 with development files + set -x -e
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/augustus/build.sh (3 hunks)
🔇 Additional comments (1)
recipes/augustus/build.sh (1)
5-8: Verify boost dependency and optimization level.While the build configuration looks correct, there are two considerations:
- The
-DUSE_BOOSTflag is added, but there should be a verification that boost is available- The
-O3optimization flag might be too aggressive for some architectures✅ Verification successful
Based on the shell script results, I can now generate the final response:
The build configuration is appropriate and follows common practices.
The verification shows:
boost-cppis correctly listed as a dependency in bothrecipes/augustus/meta.yamlandrecipes/augustus/3.3.3/meta.yaml- The
-O3optimization flag is commonly used across many bioconda packages, including similar computational biology tools like BLAST, Trinity, and other genome analysis tools🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if boost is listed as a dependency grep -r "boost-cpp" . # Check if other bioconda recipes use O3 optimization rg "CXXFLAGS.*-O3" --type shLength of output: 27028
recipes/augustus/build.sh
Outdated
| mv bin/* $PREFIX/bin/ | ||
| mv scripts/* $PREFIX/bin/ | ||
| mv config/* $PREFIX/config/ | ||
|
|
||
| make clean |
There was a problem hiding this comment.
Remove unnecessary make clean.
The make clean command after installation is unnecessary and potentially problematic:
- All required files should already be installed at this point
- Could accidentally remove files if $PREFIX points to the wrong location
-make clean📝 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.
| make clean |
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.