hifiasm: add linux-aarch64 build

[martin-g]

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[martin-g]

The Linux ARM64 build depends on:

• Linux Aarch64 support chhylp123/hifiasm#641

[martin-g]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	hifiasm-0.19.8-h43eeafb_1.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	hifiasm-0.19.8-h94ec1f5_1.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	hifiasm-0.19.8-hf1d9491_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/e6177405-efd7-4b6a-b0a1-2b310f2c215d/artifacts/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
hifiasm	0.19.8--h43eeafb_1	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/hifiasm:0.19.8--h43eeafb_1.tar.gz | docker load

[martin-g]

mgrigorov in 🌐 euler-arm-22 in /tmp/hifiasm took 5s 
❯ tar xvf hifiasm-0.19.8-hf1d9491_1.tar.bz2 
info/files
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/has_prefix
info/recipe/build.sh
info/index.json
info/paths.json
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/git
info/recipe/linux-aarch64-support.patch
bin/hifiasm

mgrigorov in 🌐 euler-arm-22 in /tmp/hifiasm 
❯ file bin/*
bin/hifiasm: 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, with debug_info, not stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/hifiasm 
❯ ./bin/hifiasm 
Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...>
Options:
  Input/Output:
    -o STR       prefix of output files [hifiasm.asm]
    -t INT       number of threads [1]
    -h           show help information
    --version    show version number
  Overlap/Error correction:
    -k INT       k-mer length (must be <64) [51]
    -w INT       minimizer window size [51]
    -f INT       number of bits for bloom filter; 0 to disable [37]
    -D FLOAT     drop k-mers occurring >FLOAT*coverage times [5.0]
    -N INT       consider up to max(-D*coverage,-N) overlaps for each oriented read [100]
    -r INT       round of correction [3]
    -z INT       length of adapters that should be removed [0]
    --max-kocc   INT
                 employ k-mers occurring <INT times to rescue repetitive overlaps [2000]
    --hg-size    INT(k, m or g)
                 estimated haploid genome size used for inferring read coverage [auto]
  Assembly:
    -a INT       round of assembly cleaning [4]
    -m INT       pop bubbles of <INT in size in contig graphs [10000000]
    -p INT       pop bubbles of <INT in size in unitig graphs [0]
    -n INT       remove tip unitigs composed of <=INT reads [3]
    -x FLOAT     max overlap drop ratio [0.8]
    -y FLOAT     min overlap drop ratio [0.2]
    -i           ignore saved read correction and overlaps
    -u           post-join step for contigs which may improve N50; 0 to disable; 1 to enable
                 [1] and [1] in default for the UL+HiFi assembly and the HiFi assembly, respectively
    --hom-cov    INT
                 homozygous read coverage [auto]
    --lowQ       INT
                 output contig regions with >=INT% inconsistency in BED format; 0 to disable [70]
    --b-cov      INT
                 break contigs at positions with <INT-fold coverage; work with '--m-rate'; 0 to disable [0]
    --h-cov      INT
                 break contigs at positions with >INT-fold coverage; work with '--m-rate'; -1 to disable [-1]
    --m-rate     FLOAT
                 break contigs at positions with <=FLOAT*coverage exact overlaps;
                 only work with '--b-cov' or '--h-cov'[0.75]
    --primary    output a primary assembly and an alternate assembly
  Trio-partition:
    -1 FILE      hap1/paternal k-mer dump generated by "yak count" []
    -2 FILE      hap2/maternal k-mer dump generated by "yak count" []
    -3 FILE      list of hap1/paternal read names []
    -4 FILE      list of hap2/maternal read names []
    -c INT       lower bound of the binned k-mer's frequency [2]
    -d INT       upper bound of the binned k-mer's frequency [5]
    --t-occ      INT
                 forcedly remove unitigs with >INT unexpected haplotype-specific reads;
                 ignore graph topology; [60]
    --trio-dual  utilize homology information to correct trio phasing errors
  Purge-dups:
    -l INT       purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]
    -s FLOAT     similarity threshold for duplicate haplotigs in read-level [0.75 for -l1/-l2, 0.55 for -l3]
    -O INT       min number of overlapped reads for duplicate haplotigs [1]
    --purge-max  INT
                 coverage upper bound of Purge-dups [auto]
    --n-hap      INT
                 number of haplotypes [2]
  Hi-C-partition:
    --h1 FILEs   file names of Hi-C R1  [r1_1.fq,r1_2.fq,...]
    --h2 FILEs   file names of Hi-C R2  [r2_1.fq,r2_2.fq,...]
    --seed INT   RNG seed [11]
    --s-base     FLOAT
                 similarity threshold for homology detection in base-level;
                 -1 to disable [0.5]; -s for read-level (see <Purge-dups>)
    --n-weight   INT
                 rounds of reweighting Hi-C links [3]
    --n-perturb  INT
                 rounds of perturbation [10000]
    --f-perturb  FLOAT
                 fraction to flip for perturbation [0.1]
    --l-msjoin   INT
                 detect misjoined unitigs of >=INT in size; 0 to disable [500000]
  Ultra-Long-integration:
    --ul FILEs   file names of Ultra-Long reads [r1.fq,r2.fq,...]
    --ul-rate    FLOAT
                 error rate of Ultra-Long reads [0.2]
    --ul-tip     INT
                 remove tip unitigs composed of <=INT reads for the UL assembly [6]
    --path-max   FLOAT
                 max path drop ratio [0.6]; higher number may make the assembly cleaner
                 but may lead to more misassemblies
    --path-min   FLOAT
                 min path drop ratio [0.2]; higher number may make the assembly cleaner
                 but may lead to more misassemblies
    --ul-cut     INT
                 filter out <INT UL reads during the UL assembly [0]
  Dual-Scaffolding:
    --dual-scaf  output scaffolding
    --scaf-gap   INT
                 max gap size for scaffolding [3000000]
Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz
See `https://hifiasm.readthedocs.io/en/latest/' or `man ./hifiasm.1' for complete documentation.

LGTM!

[martin-g]

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