spades: try to remove spades-bwa

[alienzj]

Involved packages

• spades

Involved issue

Close # 7f21e90#commitcomment-143917186

Details

• Tested in the local machine (largest 16G RAM) and it is passed without any issue
• Provide New Package
• Fix the Packages
  • PKGBUILD
  • lilac.yaml
  • lilac.py
• Would like to continue to work with us

Additional Note

1. add gcc to makedepends
2. update cmake parameters refer to https://github.com/ablab/spades/blob/main/spades_compile.sh#L225

[hubutui]

gcc is the default compiler, I don't think we need to add it.

[alienzj]

I used makepkg to test building process, then I got some errors.
After installing gcc, it works. That's why I added gcc into PKGBUILD.

[starsareintherose]

But have you tried bioarchlinux-x86_64-build?

[pekkarr]

gcc is a dependency of base-devel, so it should not be in makedepends. From Arch wiki:

The package base-devel is assumed to be already installed when building with makepkg. Dependencies of this package should not be included in makedepends array.

[alienzj]

Thanks. Removed gcc.

[starsareintherose]

my question is that the spades-bwa is same with bwa, why not use ln -s to solve it?

[alienzj]

Sorry for my misunderstanding.

From the CMakeLists.txt file https://github.com/ablab/spades/blob/main/ext/src/bwa/CMakeLists.txt#L33, it appears that SPAdes does not use the most recent version of BWA, but instead includes a method to build BWA as part of the SPAdes compilation process. This approach simplifies the installation for users, as they can compile SPAdes and have BWA built alongside it without needing to separately install BWA.

Arch Linux users, embracing the KISS principle, can opt for a simplified SPAdes installation process. If the latest BWA is compatible with SPAdes, we can remove the integrated BWA build from SPAdes and instead provide a symbolic link from spades-bwa to the latest BWA installation.

Let me try this week.
Thanks.

[alienzj]

[ 96%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o
[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o
[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o
[ 97%] Linking CXX executable ../../bin/spades-core
/usr/bin/ld: ../../common/alignment/libalignment.a(bwa_index.cpp.o): in function `alignment::BWAIndex::AlignSequence(Sequence const&, bool) const':
bwa_index.cpp:(.text+0x1f2f): undefined reference to `mem_align1_bin'
collect2: error: ld returned 1 exit status
make[2]: *** [projects/spades/CMakeFiles/spades-core.dir/build.make:186: bin/spades-core] Error 1
make[1]: *** [CMakeFiles/Makefile2:2808: projects/spades/CMakeFiles/spades-core.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
make: Leaving directory '/home/alienzj/toolkits/ohbioarchlinux/bioarchlinux/Bioarchlinux-Packages/BioArchLinux/spades/src/build'
==> ERROR: A failure occurred in build().
    Aborting..
    

After removing spades-bwa building process, there is a undefined reference to mem_align1_bin.

[alienzj]

Unfortunately,
SPAdes used:
https://github.com/ablab/spades/blob/main/src/common/alignment/bwa_index.cpp#L377
https://github.com/ablab/spades/blob/main/ext/include/bwa/bwamem.h#L153

BWA used: https://github.com/lh3/bwa/blob/master/bwamem.h

The API is not the same one.
It is difficult to use lh3's BWA directly at this moment.

[starsareintherose]

Okay, great, thanks for your testing

[starsareintherose]

you said not compatible, but why do you now use ln?

[alienzj]

I checked the API more in depth, basically, mem_align1 did same thing when compared to mem_align1_bin.

[starsareintherose]

Have you tested it with example data?