new(github.com/weizhongli/cdhit): cdhit 4.8.1#13434
Merged
Merged
Conversation
Sequence clustering (C++/OpenMP). make CC=c++ openmp=yes; gcc14 build + libstdcxx+libgomp runtime on linux; companion prot.faa.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Adds CD-HIT — sequence clustering (
cd-hit,cd-hit-est,cd-hit-2d, …). C++/OpenMP. The Makefile hardcodesCC=g++; overridden toCC=c++, builtopenmp=yes, installed withPREFIX={{prefix}}/bin(the Makefile's PREFIX is the bin dir and isn't auto-created, so the recipemkdir -ps it). On linux: gcc 14 build dep + runtimegnu.org/gcc/libstdcxxANDgnu.org/gcc/libgomp(libgomp is a separate gcc target the OpenMP binary needs; without the libstdcxx it failsGLIBCXX_3.4.3x not found). zlib is a runtime dep (links-lz). Verified on linux/arm64: builds + installs all 6 binaries,lddresolves libstdc++/libgomp from the pantry, andcd-hit -c 0.9clusters a shippedprot.faacompanion.