{bio}[foss/2024a] OrthoFinder v3.1.0, replace the bundled famsa

[wdlingit]

The current config of OrthoFinder 3.1.0 would use the bundled famsa binary, which might cause problem as mentioned in OrthoFinder/OrthoFinder#22 . This commit includes an EB file of FAMSA, adding dependency to FAMSA, and removing the bundled famsa (*).

*: it seems that OrthoFinder tries to use the bundled famsa first, no matter famsa is available in the environment or not.

[jfgrimm]

Test report by @jfgrimm
SUCCESS
Build succeeded for 8 out of 8 (total: 54 mins 20 secs) (2 easyconfigs in total)
node031.viking2.yor.alces.network - Linux Rocky Linux 8.10, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/4444f5dfc7268ba1d4540c74c05e3d1f for a full test report.

[jfgrimm]

@boegelbot: please test @ jsc-zen3

[boegelbot]

@jfgrimm: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=26137 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26137 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 10555

Test results coming soon (I hope)...

Details

- notification for comment with ID 4592700248 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (total: 15 secs) (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/f2a076695460713edd77143a6061bac1 for a full test report.

[jfgrimm]

== 2026-06-01 12:50:34,326 build_log.py:233 ERROR EasyBuild encountered an error: Checksum verification for /project/def-maintainers/boegelbot/sources/f/FAMSA/v2.5.2.tar.gz using 751d97c64524a38f2e3ded8c50a3a297fbe1c2dff0b2685e4bcedcf66d85687b failed. (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:2799 in checksum_step)

@wdlingit what python version did you run easybuild with when you generated the checksum? older python versions don't give reproducible git checksums

[jfgrimm]

@boegelbot: please test @ jsc-zen3

[boegelbot]

@jfgrimm: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=26137 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26137 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 10556

Test results coming soon (I hope)...

Details

- notification for comment with ID 4593017776 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (total: 44 secs) (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/42cb3f0af449e0d39009c84c3cb9ee16 for a full test report.

[jfgrimm]

hmm, it looks like FAMSA bundles some software in: https://github.com/refresh-bio/FAMSA/tree/master/libs
we should probably try using EB dependencies instead

[wdlingit]

hmm, it looks like FAMSA bundles some software in: https://github.com/refresh-bio/FAMSA/tree/master/libs we should probably try using EB dependencies instead

It seems that most of the dependent libraries were forked from some original versions. I am not sure whether they made individual customizations or not. The object file of mimalloc was used for making the binary (see below for the command from log). To be honest, I don't know how to apply EB dependencies for this situation. Could you please give me some idea?

g++ -o bin/famsa  \
./libs/mimalloc/mimalloc.o \
obj//famsa.cpp.o  obj//msa_refinement.cpp.o  obj//msa.cpp.o obj/core/profile_par.cpp.o  obj/core/sequence.cpp.o  obj/core/params.cpp.o  obj/core/queues.cpp.o  obj/core/profile_seq.cpp.o  obj/core/io_service.cpp.o  obj/core/profile.cpp.o obj/lcs/lcsbp.cpp.o  obj/lcs/lcsbp_classic.cpp.o obj/tree/DistanceCalculator.cpp.o  obj/tree/SingleLinkage.cpp.o  obj/tree/FastTree.cpp.o  obj/tree/MSTPrim.cpp.o  obj/tree/NeighborJoining.cpp.o  obj/tree/NewickParser.cpp.o  obj/tree/AbstractTreeGenerator.cpp.o  obj/tree/GuideTree.cpp.o  obj/tree/UPGMA.cpp.o  obj/tree/Clustering.cpp.o obj/utils/timer.cpp.o  obj/utils/utils.cpp.o  obj/utils/log.cpp.o  obj/simd/lcsbp_avx_intr.cpp.o  obj/simd/lcsbp_avx2_intr.cpp.o  obj/simd/lcsbp_avx512_intr.cpp.o  obj/simd/utils_avx.cpp.o  obj/simd/utils_avx2.cpp.o \
 ./libs/zlib-ng/build-g++/zlib-ng/libz-ng.a ./libs/libdeflate/build/libdeflate.a  -lm -lpthread -fabi-version=6   -L ./libs/zlib-ng/build-g++/zlib-ng -L ./libs/libdeflate