cd-hit: add linux-aarch64 build

[martin-g]

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[martin-g]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	cd-hit-4.8.1-h43eeafb_10.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64	cd-hit-4.8.1-h0100bc9_10.tar.bz2	OSXArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
linux-aarch64	cd-hit-4.8.1-hf1d9491_10.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/18947e83-fc71-41fe-b6be-5584d02e61e7/artifacts/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
cd-hit	4.8.1--h43eeafb_10	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/cd-hit:4.8.1--h43eeafb_10.tar.gz | docker load

[martin-g]

mgrigorov in 🌐 euler-arm-22 in /tmp/cd-hit took 4s 
❯ tar jxvf cd-hit-4.8.1-hf1d9491_10.tar.bz2 
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/index.json
info/recipe/build.sh
info/files
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/paths.json
info/about.json
info/git
bin/clstr_renumber.pl
bin/clstr_select.pl
bin/clstr_cut.pl
bin/clstr_rep.pl
bin/clstr_select_rep.pl
bin/clstr_size_stat.pl
bin/clstr_size_histogram.pl
bin/clstr_sort_by.pl
bin/cd-hit-div.pl
bin/clstr2tree.pl
bin/clstr_reduce.pl
bin/clstr_sql_tbl_sort.pl
bin/clstr_list_sort.pl
bin/clstr_reps_faa_rev.pl
bin/clstr2txt.pl
bin/clstr_sort_prot_by.pl
bin/clstr_rev.pl
bin/make_multi_seq.pl
bin/cd-hit-clstr_2_blm8.pl
bin/clstr_merge_noorder.pl
bin/plot_len1.pl
bin/clstr_quality_eval_by_link.pl
bin/clstr_sql_tbl.pl
bin/FET.pl
bin/clstr_merge.pl
bin/clstr_list.pl
bin/clstr_quality_eval.pl
bin/plot_2d.pl
bin/clstr2xml.pl
bin/cd-hit-para.pl
bin/cd-hit-2d-para.pl
bin/cd-hit-div
bin/cd-hit
bin/cd-hit-2d
bin/cd-hit-est
bin/cd-hit-est-2d
bin/cd-hit-454

mgrigorov in 🌐 euler-arm-22 in /tmp/cd-hit 
❯ file bin/*
bin/cd-hit:                        ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
bin/cd-hit-2d:                     ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
bin/cd-hit-2d-para.pl:             Perl script text executable
bin/cd-hit-454:                    ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
bin/cd-hit-clstr_2_blm8.pl:        Perl script text executable
bin/cd-hit-div:                    ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
bin/cd-hit-div.pl:                 Perl script text executable
bin/cd-hit-est:                    ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
bin/cd-hit-est-2d:                 ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
bin/cd-hit-para.pl:                Perl script text executable
bin/clstr2tree.pl:                 Perl script text executable
bin/clstr2txt.pl:                  Perl script text executable
bin/clstr2xml.pl:                  Perl script text executable
bin/clstr_cut.pl:                  Perl script text executable
bin/clstr_list.pl:                 Perl script text executable
bin/clstr_list_sort.pl:            Perl script text executable
bin/clstr_merge.pl:                Perl script text executable
bin/clstr_merge_noorder.pl:        Perl script text executable
bin/clstr_quality_eval.pl:         Perl script text executable
bin/clstr_quality_eval_by_link.pl: Perl script text executable
bin/clstr_reduce.pl:               Perl script text executable
bin/clstr_renumber.pl:             Perl script text executable
bin/clstr_rep.pl:                  Perl script text executable
bin/clstr_reps_faa_rev.pl:         Perl script text executable
bin/clstr_rev.pl:                  Perl script text executable
bin/clstr_select.pl:               Perl script text executable
bin/clstr_select_rep.pl:           Perl script text executable
bin/clstr_size_histogram.pl:       Perl script text executable
bin/clstr_size_stat.pl:            Perl script text executable
bin/clstr_sort_by.pl:              Perl script text executable
bin/clstr_sort_prot_by.pl:         Perl script text executable
bin/clstr_sql_tbl.pl:              Perl script text executable
bin/clstr_sql_tbl_sort.pl:         Perl script text executable
bin/FET.pl:                        Perl script text executable
bin/make_multi_seq.pl:             Perl script text executable
bin/plot_2d.pl:                    Perl script text executable
bin/plot_len1.pl:                  Perl script text executable

mgrigorov in 🌐 euler-arm-22 in /tmp/cd-hit 
❯ ./bin/cd-hit
		====== CD-HIT version 4.8.1 (built on Apr 11 2024) ======

Usage: ./bin/cd-hit [Options] 

Options

   -i	input filename in fasta format, required, can be in .gz format
   -o	output filename, required
   -c	sequence identity threshold, default 0.9
 	this is the default cd-hit's "global sequence identity" calculated as:
 	number of identical amino acids or bases in alignment
 	divided by the full length of the shorter sequence
   -G	use global sequence identity, default 1
 	if set to 0, then use local sequence identity, calculated as :
 	number of identical amino acids or bases in alignment
 	divided by the length of the alignment
 	NOTE!!! don't use -G 0 unless you use alignment coverage controls
 	see options -aL, -AL, -aS, -AS
   -b	band_width of alignment, default 20
   -M	memory limit (in MB) for the program, default 800; 0 for unlimitted;
   -T	number of threads, default 1; with 0, all CPUs will be used
   -n	word_length, default 5, see user's guide for choosing it
   -l	length of throw_away_sequences, default 10
   -t	tolerance for redundance, default 2
   -d	length of description in .clstr file, default 20
 	if set to 0, it takes the fasta defline and stops at first space
   -s	length difference cutoff, default 0.0
 	if set to 0.9, the shorter sequences need to be
 	at least 90% length of the representative of the cluster
   -S	length difference cutoff in amino acid, default 999999
 	if set to 60, the length difference between the shorter sequences
 	and the representative of the cluster can not be bigger than 60
   -aL	alignment coverage for the longer sequence, default 0.0
 	if set to 0.9, the alignment must covers 90% of the sequence
   -AL	alignment coverage control for the longer sequence, default 99999999
 	if set to 60, and the length of the sequence is 400,
 	then the alignment must be >= 340 (400-60) residues
   -aS	alignment coverage for the shorter sequence, default 0.0
 	if set to 0.9, the alignment must covers 90% of the sequence
   -AS	alignment coverage control for the shorter sequence, default 99999999
 	if set to 60, and the length of the sequence is 400,
 	then the alignment must be >= 340 (400-60) residues
   -A	minimal alignment coverage control for the both sequences, default 0
 	alignment must cover >= this value for both sequences 
   -uL	maximum unmatched percentage for the longer sequence, default 1.0
 	if set to 0.1, the unmatched region (excluding leading and tailing gaps)
 	must not be more than 10% of the sequence
   -uS	maximum unmatched percentage for the shorter sequence, default 1.0
 	if set to 0.1, the unmatched region (excluding leading and tailing gaps)
 	must not be more than 10% of the sequence
   -U	maximum unmatched length, default 99999999
 	if set to 10, the unmatched region (excluding leading and tailing gaps)
 	must not be more than 10 bases
   -B	1 or 0, default 0, by default, sequences are stored in RAM
 	if set to 1, sequence are stored on hard drive
 	!! No longer supported !!
   -p	1 or 0, default 0
 	if set to 1, print alignment overlap in .clstr file
   -g	1 or 0, default 0
 	by cd-hit's default algorithm, a sequence is clustered to the first 
 	cluster that meet the threshold (fast cluster). If set to 1, the program
 	will cluster it into the most similar cluster that meet the threshold
 	(accurate but slow mode)
 	but either 1 or 0 won't change the representatives of final clusters
   -sc	sort clusters by size (number of sequences), default 0, output clusters by decreasing length
 	if set to 1, output clusters by decreasing size
   -sf	sort fasta/fastq by cluster size (number of sequences), default 0, no sorting
 	if set to 1, output sequences by decreasing cluster size
 	this can be very slow if the input is in .gz format
   -bak	write backup cluster file (1 or 0, default 0)
   -h	print this help

   Questions, bugs, contact Weizhong Li at [email protected]
   For updated versions and information, please visit: http://cd-hit.org
                                                    or https://github.com/weizhongli/cdhit

   cd-hit web server is also available from http://cd-hit.org

   If you find cd-hit useful, please kindly cite:

   "CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659
   "CD-HIT: accelerated for clustering the next generation sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152

LGTM!

[martin-g]

@BiocondaBot please add label

[ori-scala]

@martin-g Would you be able to add support for osx-arm64?

[mencian]

@ori-scala added osx-arm64 build to cd-hit here; the osx-arm64 build should be available now.