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* Add scsplit (bioconda#46438)

* changes to cellhashr

* yaml file for scsplit

* out cellhashr folder

* Lint fix

* fix lint

* fix lint

* corrections for lint

* fixes lowercase

* scsplit out

* scsplit back

* change to link

* fixes

* cutadapt: add linux-aarch64 build (bioconda#46424)

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* bump revoluzer 0.1.6 (bioconda#46517)

* Update pyhmmer to 0.10.10 (bioconda#46518)

* Update compleasm to 0.2.6 (bioconda#46532)

* Update sevenbridges-python to 2.11.0 (bioconda#46531)

* Update rnachipintegrator to 3.0.0 (bioconda#46520)

* Update rnachipintegrator to 3.0.0

* rnachipintegrator: add missing 'run_exports' statements required by linter.

---------

Co-authored-by: Peter Briggs <peter.briggs@manchester.ac.uk>

* Update ena-webin-cli to 7.1.1 (bioconda#46530)

* Update sneep to 1.0 (bioconda#46528)

* Update physiofit to 3.3.5 (bioconda#46526)

* Update pcaone to 0.4.4 (bioconda#46521)

* fasttree: add linux-aarch64 build (bioconda#46436)

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* fix busco patch (bioconda#46524)

* fix busco patch

* increment build number

* Update r-acidgenerics to 0.7.7 (bioconda#46536)

* Update r-acidplyr to 0.5.4 (bioconda#46538)

* Update checkqc to 4.0.1 (bioconda#46529)

* Update checkqc to 4.0.1

* add python to run deps as package is noarch:python

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update trust4 to 1.0.14 (bioconda#46537)

* Fix entrypoint for psm-utils (bioconda#46533)

* update python-edlib: enable python-edlib build (bioconda#46513)

* muscle: add linux-aarch64 build (bioconda#46525)

* muscle: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Bump muscle to 5.1.0

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Add support for Linux ARM64

rcedgar/muscle#73

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* hmmcopy: enable linux-aarch64 build (bioconda#46359)

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* linux-aarch64 build for alcor (bioconda#46388)

* linux-aarch64 build for alcor

* linux-aarch64 build for alcor

* linux-aarch64 build for alcor

* linux-aarch64 build for alcor

* linux-aarch64 build for ac (bioconda#46362)

* linux-aarch64 build for ac

* linux-aarch64 build for ac

* Update treeswift to 1.1.40 (bioconda#46541)

* Update phykit to 1.19.0 (bioconda#46542)

* Update r-azimuth to 0.5.0 (bioconda#46495)

* Update r-azimuth to 0.5.0

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: Christian Brueffer <christian@brueffer.io>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update augur to 24.3.0 (bioconda#46534)

* Update psm-utils to 0.7.4 (bioconda#46535)

* Update psm-utils to 0.7.4

* reset build number

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update freyja to 1.5.0 (bioconda#46544)

* Update mgatk recipe (bioconda#46545)

* Update maegatk recipe (bioconda#46546)

* Update yacht to 1.2.2 (bioconda#46547)

* bowtie2: add linux-aarch64 build (bioconda#46423)

* bowtie2: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* bowtie2: [linux-aarch64] Git clone the third party dependencies

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* pyspoa: enable linux-aarch64 build (bioconda#46549)

* pyrodigal: enable linux-aarch64 build (bioconda#46553)

* pyrodigal: enable linux-aarch64 build

* bump build number

* Update phold to 0.1.3 (bioconda#46557)

* Update snakemake to 8.9.0 (bioconda#46565)

* pyhmmer: enable linux-aarch64 build (bioconda#46551)

* Update bioconda-utils to 2.12.0 (bioconda#46577)

* update fastp adding new platform (bioconda#46576)

* update stringtie adding new platform (bioconda#46569)

* update stringtie adding new platform

* add run_exports

* add zlib

* make linux-aarch64 build for age_metasv (bioconda#46563)

* linux-aarch64 build for age-metasv

* linux-aarch64 build for age-metasv

---------

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* Add srahunter/meta.yaml (bioconda#46243)

* Changes to be committed:
	new file:   srahunter/meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* update star adding new platform (bioconda#46555)

* update star adding new platform

* fix make flags

* Update assemblycomparator2 to 2.6.1 (bioconda#46566)

* Update boms to 1.1.0 (bioconda#46571)

* Update perl-minion to 10.29 (bioconda#46579)

* Add recipe hairsplitter (bioconda#46564)

* added hairsplitter

* correct linting

* corrected hairsplitter recipe

* Update diffacto to 1.0.7 (bioconda#46561)

* Update diffacto to 1.0.7

* add run_exports

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update tracegroomer to 0.1.3 (bioconda#46583)

* Update genomad to 1.7.6 (bioconda#46589)

* Update genomad to 1.7.6

* edit run_exports

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* pybigwig: enable linux-aarch64 build (bioconda#46588)

* pyfamsa: enable linux-aarch64 build (bioconda#46582)

* bx-python: enable linux-aarch64 build (bioconda#46584)

* parasail-python: enable linux-aarch64 build (bioconda#46585)

* pyabpoa: enable linux-aarch64 build (bioconda#46586)

* cyvcf2: enable linux-aarch64 build (bioconda#46591)

* Update fibertools-rs to 0.4.1 (bioconda#46593)

* Updated ToulligQC to v2.5.3 (bioconda#46574)

* Updated ToulligQC to v2.5.3 and dependencies

* Update matplotlib to matplotlib-base

* Changed python 3.11.0 to 3.10.0

* Remove pip

* Incorrect sha256

* Update pixelator to 0.16.2 (bioconda#46606)

* update preseq adding new platform (bioconda#46596)

* update preseq adding new platform

* skip for osx-arm64

* Revert "skip for osx-arm64"

This reverts commit 506b52a.

* linux-aarch64 build for bioawk (bioconda#46604)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* linux-aarch64 build for bedops (bioconda#46603)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* linux-aarch64 build for bedtk (bioconda#46602)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* linux-aarch64 build for bfc (bioconda#46601)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* linux-aarch64 build for bcalm (bioconda#46600)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* update fq adding new platform (bioconda#46599)

* update gffread adding new platform (bioconda#46595)

* linux-aarch64 build for aragorn (bioconda#46592)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* Update pathogen-profiler to 4.1.0 (bioconda#46612)

* Update pathogen-profiler to 4.1.0

* update deps and shasum

---------

Co-authored-by: Jody Phelan <jody.phelan@lshtm.ac.uk>

* update bedgraphtobigwig with additional platform (bioconda#46516)

* add additional platform

* increase build number

* add patch

* fix typo

---------

Co-authored-by: Pablo <pablo.aledo@gmail.com>

* Update pymlst to 2.1.6 (bioconda#46615)

* Update hmftools-orange to 3.3.1 (bioconda#46614)

* Update skyline2isocor to 1.0.0 (bioconda#46608)

* Update pybiolib to 1.1.1881 (bioconda#46616)

* linux-aarch64 build for addrg (bioconda#46609)

* linux-aarch64 build for addrg
* Set max_pin to x.x
* Add zlib developer dependency

---------

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* Add linux-aarch64 build for seqkit (bioconda#46620)

* Add SigProfilerPlotting recipe (bioconda#46607)

* Add SigProfilerPlotting recipe

* update test command

* Update meta.yaml

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Update: Musgy - Fix issue with sed on macos m1 (bioconda#46625)

* Update meta.yaml

attempt to fix sed issue on macos m1

* Update meta.yaml

added run_exports for linting check

* add linux-aarch64-aligncov

* add linux-aarch64-aligncov

* Update tb-profiler to 6.1.0 (bioconda#46622)

* Update mosdepth to 0.3.7 (bioconda#46627)

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* Update mitos to 2.1.8 (bioconda#46639)

* bump baredsc to test build (bioconda#46613)

* bump baredsc to test build

* unbump baredsc

* add space to rebuild

* Add SigProfilerMatrixGenerator recipe (bioconda#46605)

* recipe added

* run_exports added

* Recipe update

* test commands update

* Update prokbert to 0.0.44 (bioconda#45794)

* Update prokbert to 0.0.41

* Update prokbert to 0.0.43

* Update prokbert to 0.0.44

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update ampcombi to 0.2.2 (bioconda#46641)

* Update hmftools-mark-dups to 1.1.3 (bioconda#46628)

* Update treetime to 0.11.3 (bioconda#46647)

* Update ppanggolin to 2.0.5 (bioconda#46648)

* Update ebi-eva-common-pyutils to 0.6.4 (bioconda#46645)

* ltr_harvest_parallel: Removed ver for genometools-genometools (bioconda#46623)

* Removed ver for genometools-genometools

* Incremented build number

* Removed ver constraint for ltr_finder (bioconda#46624)

* Add splitcode recipe (bioconda#46543)

* Add splitcode recipe

* Add splitcode recipe: set build number 0

* Update recipes/splitcode/meta.yaml

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>

---------

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>

* Update agc to 3.1 (bioconda#46540)

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update recipes/agc/meta.yaml

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Ryan Dale <ryan.dale@nih.gov>

* Update agat to 1.3.2 (bioconda#46652)

* Update anchorwave to 1.2.3 (bioconda#46631)

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update itsxpress to 2.0.2 (bioconda#46654)

* Update snakemake-interface-executor-plugins to 9.0.1 (bioconda#46651)

* bimp mitos (bioconda#46638)

* Update meta.yaml (bioconda#46619)

* Update ms2deepscore to 2.0.0 (bioconda#46637)

* Update ms2deepscore to 2.0.0

* update dependencies

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update callingcardstools to 1.5.2 (bioconda#46657)

* Update fibertools-rs to 0.4.2 (bioconda#46660)

* update tb-profiler dependencies (bioconda#46649)

* update dependencies

* update build number

* Update TREE-QMC to 3.0.0 (bioconda#46656)

* tqmc

* build.sh fixed

* "folder_and_package_name_must_match" fixed

* missing_run_exports fixed

* g++ not found fix

* build error fixed

* build error fix

* build.sh fix

* osx compilation fix

* made the name and version number consistent

* minor

* tree-qmc 3.0.0 updates

* tree-qmc 3.0.0 updates

* build.sh fixed

* build.sh fixed

* build.sh fixed

* build.sh

* build.sh

* debug

* build

* Update sourmash to 4.8.7 (bioconda#46655)

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* linux-aarch64 build for 3seq (bioconda#46610)

* linux-aarch64 build for 3seq

* updated pin_subpackage

---------

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>
Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>

* linux-aarch64 build for abundancebin (bioconda#46633)

Co-authored-by: HWsunqian0027 <sunny_sunqian@163.com>

* update ucsc-bedclip adding new platform (bioconda#46626)

* update ucsc-bedclip adding new platform

* add patch

* fix compilation for arm

* remove from blacklist

* try another way to specify compiler version

* edit pin_subpackage

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update ntsynt build (bioconda#46659)

* Update ntlink build (bioconda#46663)

* Pinning btllib version for now due to possible bug in the most recent release

* Update r-liger to 2.0.0 (bioconda#46621)

* Update r-liger to 2.0.0

* add missing deps

* oops, bioconductor- not r-

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update oakvar to 2.9.92 (bioconda#46668)

* Update comet-ms from v2023.01.0 to v2023.01.2 (bioconda#46567)

* Update meta.yaml

* Update build number and run_exports

* add -lrt to makefile due to chrono error

* add escapes in build.sh

* Update build.sh

* Update build.sh

* Update recipes/comet-ms/build.sh

Co-authored-by: Julianus Pfeuffer <julianus.pfeuffer@pfizer.com>

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Create conda_build_config.yaml to control glibc version during test

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Delete recipes/comet-ms/conda_build_config.yaml

* Update meta.yaml

* ad gcc to build (which implicitely adds libgcc during host and runtime)

* static with glibc 2.17

---------

Co-authored-by: Julianus Pfeuffer <julianus.pfeuffer@pfizer.com>

* Update snakemake-interface-executor-plugins to 9.0.2 (bioconda#46684)

* Update sequali to 0.5.1 (bioconda#46694)

* Update ntm-profiler to 0.4.0 (bioconda#46667)

* Update ntm-profiler to 0.4.0

* Update pathogen profiler pinning

* update deps

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Jody Phelan <jody.phelan@lshtm.ac.uk>

* Updated ToulligQc to v2.5.4 (bioconda#46689)

* linux-aarch64 build for mappy (bioconda#46674)

Co-authored-by: yejianbang <yjb_kunpeng@163.com>

* inux-aarch64 build for altair-mf (bioconda#46673)

* linux-aarch64 build for altair-mf

* Update meta.yaml

---------

Co-authored-by: yejianbang <yjb_kunpeng@163.com>
Co-authored-by: yejianbang <145335562+yejianbang@users.noreply.github.com>

* Update pbstarphase to 0.8.2 (bioconda#46699)

* Update snakemake-executor-plugin-lsf to 0.2.3 (bioconda#46693)

* Update bactopia-py to 1.0.9 (bioconda#46704)

* Update phables to 1.3.2 (bioconda#46676)

* Update zol to 1.3.20 (bioconda#46709)

* moved arborator v1.0.0 (bioconda#46650)

arborator v1.0.0

moved arborator to the right folder

* Update wfmash to 0.13.0 (bioconda#46710)

* Add recipe for REViewer (bioconda#46514)

* Update meta.yaml (bioconda#46711)

* update rgi pinning for pyrodigal (bioconda#46669)

* update rgi pinning for pyrodigal

* bump build number

* fix issue with sistr container (bioconda#46712)

* fix issue with sistr container

* fix typo

* adjust python pinning in gubbins (bioconda#46713)

* fix amrfinderplus pinning in abritamr (bioconda#46714)

* locidex v0.1.1 recipe (bioconda#46715)

* locidex v0.0.1 recipe

* locidex v0.0.1 recipe

* locidex v0.1.1 recipe

* locidex v0.1.1 recipe

* Add new package for genotyping reads (bioconda#46587)

* Add new package for genotyping reads

* Changed python version to 3.8

* Updated python version

* Updated dependencies

* Updated biopython version

* Removed build.sh

* Update meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Updated meta.yaml

* Update meta.yaml

* Minor changes

* Minor change

* Version update

* Update neat to 4.1.1 (bioconda#46708)

* Update neat to 4.1

* Update neat to 4.1.1

* Update massdash to 0.0.9 (bioconda#46707)

* Update pbfusion to 0.4.1 (bioconda#46705)

* Update hifihla to 0.3.0 (bioconda#46702)

* Update snakemake to 8.10.0 (bioconda#46691)

* Update snakemake to 8.10.0

* Update meta.yaml

---------

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

* Update chewbbaca to 3.3.4 (bioconda#46698)

* Update fiji-simple_omero_client to 5.18.0 (bioconda#46700)

* Update dxpy to 0.372.0 (bioconda#46692)

* Update dimet to 0.2.4 (bioconda#46685)

* Update viroconstrictor to 1.4.1 (bioconda#46682)

* update taxor to version 0.1.3 (bioconda#46678)

Co-authored-by: Jens-Uwe Ulrich <jens-uwe.ulrich@hpi.de>

* Update hictk to v0.0.11 (bioconda#46703)

* Bump hictk to v0.0.11

* Compiler segfaults are so much fun...

* WIP

* WIP

* WIP

* WIP

* Bugfix

* Update URL and checksum

* Update dragonflye to 1.2.0 (bioconda#46721)

* Update dragonflye to 1.2.0

* Update depends

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Update bactopia-assembler to 1.0.4 (bioconda#46720)

* Update bactopia-assembler to 1.0.4

* Update depends

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Update pangu to 0.2.5 (bioconda#46701)

* Update bactopia to 3.0.1 (bioconda#46724)

* Update bactopia to 3.0.1

* Update depends

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Update tb-profiler to 6.2.0 (bioconda#46732)

* add linux-aarch64-alignoth (bioconda#46646)

* add linux-aarch64-aligncov

* add linux-aarch64-aligncov

* alignoth

* alignoth2

* alignoth2

* alignoth2

---------

Co-authored-by: yejianbang <yjb_kunpeng@163.com>

* Update DRAM version (bioconda#46723)

* Update dram version

* Add github issue link

* Add run_exports

* Fix patches location

* Fix patch

---------

Co-authored-by: Natasha Pavlovikj <npavlovikj2@unl.edu>

* Update resfinder to 4.5.0 (bioconda#46681)

* Update rmats to 4.3.0 (bioconda#46695)

* Update pybiolib to 1.1.1909 (bioconda#46688)

* Update pybiolib to 1.1.1890

* Update pybiolib to 1.1.1892

* Update pybiolib to 1.1.1896

* Update pybiolib to 1.1.1909

* Update gnparser to 1.9.1 (bioconda#46683)

* Update cazy_webscraper to 2.3.0.3 (bioconda#46725)

* Update influx-si-data-manager to 1.0.1 (bioconda#46737)

* Add lemur v1.0.0 (bioconda#46666)

* Add lemur v1.0.0

* Add run_exports

* Add eva-sub-cli recipe (bioconda#45929)

* add eva-sub-cli recipe

* fix indentation

* add unzip

* quiet unzip

* add preserve_egg_dir

* add node to run requirements

* update meta with new conda dependencies

* trigger pipeline

* bamtools: add linux-aarch64 build (bioconda#46734)

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Update TREE-QMC to 3.0.1 (bioconda#46738)

* tqmc

* build.sh fixed

* "folder_and_package_name_must_match" fixed

* missing_run_exports fixed

* g++ not found fix

* build error fixed

* build error fix

* build.sh fix

* osx compilation fix

* made the name and version number consistent

* minor

* tree-qmc 3.0.0 updates

* tree-qmc 3.0.0 updates

* build.sh fixed

* build.sh fixed

* build.sh fixed

* build.sh

* build.sh

* debug

* build

* v3.0.1

* seqtk: add linux-aarch64 build (bioconda#46730)

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Update dajin2 to 0.4.2 (bioconda#46722)

* update dimet for Ben (bioconda#46739)

* Update bioconda-utils to 2.13.0 (bioconda#46740)

* Update bioconda-utils to 2.13.0

* update requirements to match bioconda-utils repo

---------

Co-authored-by: aliciaaevans <alicia.evans@nih.gov>

* Update influx-si-data-manager to 1.0.2 (bioconda#46741)

* Update vcfdist to 2.5.1 (bioconda#46743)

* linux-aarch64 build for alignstats (bioconda#46635)

* linux-aarch64 build for alignstats

* linux-aarch64 build for alignstats

* Update meta.yaml

---------

Co-authored-by: yejianbang <yjb_kunpeng@163.com>
Co-authored-by: yejianbang <145335562+yejianbang@users.noreply.github.com>

* update umi_tools adding new platform (bioconda#46598)

* updated pyrodigal >=3.0 due to new feature for locidex (bioconda#46742)

* Update condiga to 0.2.2 (bioconda#46675)

* Update condiga to 0.2.2

* add run_exports

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update anvio-minimal to 8 (bioconda#43417)

* Update anvio-minimal to 8

* Update anvio-minimal to 8

* add run_exports

* edit dependencies

* Update anvio-minimal to 8

* Update anvio-minimal to 8

* Update anvio-minimal to 8

* add multiprocess

* add rich-argparse

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* Update hapog to 1.3.8 (bioconda#46680)

* Update hapog to 1.3.8

* add zlib

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update magus-msa to 0.2.0 (bioconda#46726)

* Update magus-msa to 0.2.0

* edit tests

* edit tests

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* Update treeqmc to 3.0.1 (bioconda#46696)

* Update treeqmc to 3.0.1

* Update treeqmc to 3.0.3

* update meta.yaml

* add recipe to blacklist

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* update ucsc-bedclip (bioconda#46686)

* remove specific cpu flag

* bump build number

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

* add treeqmc to blacklist (bioconda#46746)

* Update gmap to 2024.03.15 (bioconda#46745)

* Update gmap to 2024.03.15

* edit build.sh

* revert to skipping OSX & enable aarch64 build

* revert to linux only

* Update arcs to 1.2.7 (bioconda#46749)

* Update scib recipe (bioconda#46748)

* Update phold to 0.1.4 (bioconda#46751)

* Update pangu to 0.2.6 (bioconda#46752)

* Harpy 0.8.0 + recipe change (bioconda#46658)

* update build recipe

* specify current version

* raxml: add linux-aarch64 build (bioconda#46469)

* raxml: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Disable the tests which are x86_64/AVX specific

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* try build selector

* try build selector

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

* wfa2-lib: enable linux-aarch64 build (bioconda#46753)

* wfa2-lib: enable linux-aarch64 build

* edit build.sh

* edit build.sh

* edit build.sh

* edit build.sh

* edit build.sh

* tabixpp: enable linux-aarch64 build (bioconda#46754)

* tabixpp: enable linux-aarch64 build

* try without patch

* try without patch 2

* linux-aarch64 build for adapterremoval

* fix

* linux-aarch64 build for dbg2olc

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: Mylène Mariana Gonzales André <103585173+mari-ga@users.noreply.github.com>
Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: M Bernt <m.bernt@ufz.de>
Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Co-authored-by: Peter Briggs <peter.briggs@manchester.ac.uk>
Co-authored-by: Matthew Berkeley <42berkeley@cua.edu>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Ralf Gabriels <ralfg@hotmail.be>
Co-authored-by: guozhicong <juiceonion@foxmail.com>
Co-authored-by: sunqian2002 <50086972+huazhong28@users.noreply.github.com>
Co-authored-by: Christian Brueffer <christian@brueffer.io>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: pabloaledo <112545720+pabloaledo@users.noreply.github.com>
Co-authored-by: sunqian2116 <163837843+sunqian2116@users.noreply.github.com>
Co-authored-by: Enrico <75318813+GitEnricoNeko@users.noreply.github.com>
Co-authored-by: RolandFaure <64131971+RolandFaure@users.noreply.github.com>
Co-authored-by: Salomé Brunon <91611978+Salome-Brunon@users.noreply.github.com>
Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>
Co-authored-by: Jody Phelan <jody.phelan@lshtm.ac.uk>
Co-authored-by: Pablo <pablo.aledo@gmail.com>
Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>
Co-authored-by: Paweł <38688203+pawelqs@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Ammar Aziz <spidermine63@gmail.com>
Co-authored-by: yejianbang <yjb_kunpeng@163.com>
Co-authored-by: tamuanand <tamuanand@users.noreply.github.com>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
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Co-authored-by: Usman Rashid <usman@smme.edu.pk>
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Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
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Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>
Co-authored-by: Lauren Coombe <lauren.e.coombe@gmail.com>
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Co-authored-by: Jens Luebeck <jluebeck@ucsd.edu>
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Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
Co-authored-by: Jens-Uwe Ulrich <46562264+JensUweUlrich@users.noreply.github.com>
Co-authored-by: Jens-Uwe Ulrich <jens-uwe.ulrich@hpi.de>
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4 changes: 3 additions & 1 deletion build-fail-blacklist
Original file line number Diff line number Diff line change
Expand Up @@ -802,7 +802,6 @@ recipes/ucsc-axtsort
recipes/ucsc-axtswap
recipes/ucsc-axttomaf
recipes/ucsc-bamtopsl
recipes/ucsc-bedclip
recipes/ucsc-bedcommonregions
recipes/ucsc-bedcoverage
recipes/ucsc-bedextendranges
Expand Down Expand Up @@ -1062,3 +1061,6 @@ recipes/mudskipper

# md5 mismatch when downloading source
recipes/komb

# duplicate recipe
recipes/treeqmc
10 changes: 8 additions & 2 deletions recipes/3seq/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,9 @@ package:
version: {{ version }}

build:
number: 3
number: 4
run_exports:
- {{ pin_subpackage("3seq", max_pin="x") }}

source:
url: https://gitlab.com/lamhm/{{ name|lower }}/-/archive/v{{ version }}/3seq-v{{ version }}.tar.gz
Expand All @@ -28,6 +30,10 @@ test:

about:
home: https://mol.ax/software/3seq/
license: CC BY-NC-SA 4.0
license: CC-BY-NC-SA-4.0
license_file: LICENSE.md
summary: '3SEQ tests all sequence triplets in an alignment for a mosaic recombination signal.'

extra:
additional-platforms:
- linux-aarch64
7 changes: 5 additions & 2 deletions recipes/abritamr/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ source:
sha256: "{{ sha256 }}"

build:
number: 0
number: 1
noarch: python
entry_points:
- abritamr=abritamr.abritamr:main
Expand All @@ -29,7 +29,10 @@ requirements:
- python >=3.9
- pandas
- xlsxwriter
- ncbi-amrfinderplus =3.10.42
# Please review ncbi-amrfinderplus pinning every release
# The version should be pinned to the database version used by abritamr
# Please see the "changes.txt" file in https://github.com/MDU-PHL/abritamr/blob/master/abritamr/db/amrfinderplus/data/<DATABASE_VERSION>/changes.txt
- ncbi-amrfinderplus =3.12.8
- blast
- hmmer

Expand Down
6 changes: 5 additions & 1 deletion recipes/abundancebin/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@ source:
- 0001-Use-CXX-and-flags.patch

build:
number: 6
number: 7
run_exports:
- {{ pin_subpackage("abundancebin", max_pin="x.x.x") }}
skip: True # [osx]

requirements:
Expand Down Expand Up @@ -45,3 +47,5 @@ extra:
- keuv-grvl
identifiers:
- doi:10.1007/978-3-642-12683-3_35
additional-platforms:
- linux-aarch64
8 changes: 7 additions & 1 deletion recipes/ac/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,9 @@ package:
build:
# Passes some invalid flags for clang
skip: True # [osx]
number: 4
number: 5
run_exports:
- {{ pin_subpackage("ac", max_pin="x.x") }}

source:
url: https://github.com/cobilab/ac/archive/v{{ version }}.tar.gz
Expand All @@ -30,3 +32,7 @@ about:
license_file: LICENSE
license_family: GPL
summary: A lossless compression tool for Amino Acid sequences

extra:
additional-platforms:
- linux-aarch64
8 changes: 7 additions & 1 deletion recipes/adapterremoval/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,9 @@ source:
sha256: {{ sha256 }}

build:
number: 2
number: 3
run_exports:
- {{ pin_subpackage("adapterremoval", max_pin="x.x.x") }}

requirements:
build:
Expand All @@ -34,3 +36,7 @@ about:
license: GPL3
license_file: LICENSE
summary: The AdapterRemoval v2 tool for merging and clipping reads.

extra:
additional-platforms:
- linux-aarch64
9 changes: 8 additions & 1 deletion recipes/addrg/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,9 @@ package:
version: {{ version }}

build:
number: 11
number: 12
run_exports:
- {{ pin_subpackage("addrg", max_pin="x.x") }}

source:
url: https://github.com/holtgrewe/addrg/archive/v{{ version }}.tar.gz
Expand All @@ -17,6 +19,7 @@ requirements:
- {{ compiler('c') }}
host:
- htslib
- zlib
run:
- htslib

Expand All @@ -28,3 +31,7 @@ about:
home: https://github.com/holtgrewe/addrg
license: MIT
summary: Add read group to BAM files

extra:
additional-platforms:
- linux-aarch64
4 changes: 2 additions & 2 deletions recipes/agat/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "AGAT" %}
{% set version = "1.3.1" %}
{% set sha256 = "0361f5f5708b0010045a410e3656d6b16571d5ebaf72898f6df846c49f282a3c" %}
{% set version = "1.3.2" %}
{% set sha256 = "f5ceadceca0ad8b423e51c199a6ae66921b88021ebf969c971da59df53b72fc5" %}

package:
name: "{{ name|lower }}"
Expand Down
24 changes: 16 additions & 8 deletions recipes/agc/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,20 +1,26 @@
{% set version = "3.0" %}
{% set system = "linux"%} # [linux]
{% set system = "mac"%} # [osx]
{% set sha256 = "3ee3245e556221d246f9afe5d9ad86888f4eb5aea6b10f621241c3170ef8835e" %} # [linux]
{% set sha256 = "3d68b6b76948b6d9a36c4e848e37969eda6ae0ec1abace4ca61a7cc585dcdabf" %} # [osx]
{% set version = "3.1" %}

package:
name: agc
version: {{ version }}

build:
number: 0
script: "mkdir -p ${PREFIX}/bin; cp agc ${PREFIX}/bin"
run_exports:
- {{ pin_subpackage('agc', max_pin="x") }}
source:
url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64-{{ system }}.tar.gz
sha256: {{ sha256 }}
- url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_arm_linux.tar.gz # [aarch64]
sha256: 5fee3ccbb2691d82a877987e204c5946dbdbe40b9603af5d2421cb8506577534 # [aarch64]
- url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_linux.tar.gz # [linux64]
sha256: 4868dd45c1ed31a7f36bcbc536174249de27b87ec83858d22b128cbec8deef53 # [linux64]
- url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_mac.tar.gz # [osx and x86_64]
sha256: 0ef911e6bb8df791593ee6e89b5bddbf82b5823684955d249d6a67a39e6d0d4e # [osx and x86_64]
- url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_m1_mac.tar.gz # [osx and arm64]
sha256: ff8cc5dd4c5825a41e042567a93e9e01ef43fc91624c983640a29fd3c7ac03e4 # [osx and arm64]
requirements:
build:
run:
run:
about:
home: https://github.com/refresh-bio/agc
summary: "Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans)."
Expand All @@ -23,6 +29,8 @@ test:
commands:
- agc
extra:
additional-platforms:
- linux-aarch64
skip-lints:
- should_be_noarch_generic
- should_not_be_noarch_source
Expand Down
9 changes: 8 additions & 1 deletion recipes/age-metasv/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,17 @@ source:

build:
skip: True # [osx]
number: 7
number: 8
run_exports:
- {{ pin_subpackage("age-metasv", max_pin="x.x.x") }}

requirements:
build:
- make
- {{ compiler('cxx') }}
- llvm-openmp # [osx]
- libgomp # [linux]
- libstdcxx-ng >=12
host:
run:

Expand All @@ -29,3 +32,7 @@ about:
home: https://github.com/marghoob/AGE/tree/simple-parseable-output
license: CCPL (Creative Commons Public License)
summary: optimal alignment of sequences with structural variants (SVs), modifiied for MetaSV integration

extra:
additional-platforms:
- linux-aarch64
8 changes: 7 additions & 1 deletion recipes/alcor/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,9 @@ package:
build:
# Passes some invalid flags for clang
skip: True # [osx]
number: 2
number: 3
run_exports:
- {{ pin_subpackage("alcor", max_pin="x.x") }}

source:
url: https://github.com/cobilab/alcor/archive/v{{ version }}.tar.gz
Expand All @@ -37,3 +39,7 @@ about:
license_file: LICENSE
license_family: GPL
summary: Software for alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.

extra:
additional-platforms:
- linux-aarch64
5 changes: 4 additions & 1 deletion recipes/alignoth/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ package:
version: {{ version }}

build:
number: 0
number: 1
# TODO fails to build on osx with
# Undefined symbols for architecture x86_64: "_SSLCopyALPNProtocols", referenced from: _sectransp_connect_step2 in libcurl_sys-1f07db570920ba9f.rlib(sectransp.o)
skip: true #[osx]
Expand All @@ -30,6 +30,7 @@ requirements:
- libcurl
- openssl


test:
commands:
- alignoth --help
Expand All @@ -43,3 +44,5 @@ extra:
recipe-maintainers:
- fxwiegand
- johanneskoester
additional-platforms: #add aarch64
- linux-aarch64
8 changes: 7 additions & 1 deletion recipes/alignstats/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,9 @@ source:
sha256: {{ sha256 }}

build:
number: 1
number: 2
run_exports:
- {{ pin_subpackage("alignstats", max_pin="x.x.x") }}

requirements:
build:
Expand All @@ -33,3 +35,7 @@ about:
home: https://github.com/jfarek/alignstats
license: BSD-3-Clause
summary: Comprehensive alignment, whole-genome coverage, and capture coverage statistics.

extra:
additional-platforms:
- linux-aarch64
8 changes: 7 additions & 1 deletion recipes/altair-mf/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,9 @@ package:
build:
# Passes some invalid flags for clang
skip: True # [osx]
number: 2
number: 3
run_exports:
- {{ pin_subpackage("altair-mf", max_pin="x.x.x") }}

source:
url: https://github.com/cobilab/altair/archive/v{{ version }}.tar.gz
Expand All @@ -37,3 +39,7 @@ about:
license_file: LICENSE
license_family: GPL
summary: Software for alignment-free and spatial-temporal analysis of multi-FASTA data

extra:
additional-platforms:
- linux-aarch64
4 changes: 2 additions & 2 deletions recipes/ampcombi/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{% set name = "AMPcombi" %}
{% set version = "0.2.1" %}
{% set version = "0.2.2" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
sha256: da699d66190e654b6c9ca333228678fd759f4ce8e84b8022c24417cf5a300c86
sha256: da9a179851a8f2041d05ccd10dd45b58099e84059e2e66a9ee405d1913471b58

build:
noarch: python
Expand Down
14 changes: 8 additions & 6 deletions recipes/ampliconsuite/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{% set name="ampliconsuite" %}
{% set AS_version="1.2.2" %}
{% set AA_version="1.3.r8" %}
{% set AC_version="1.1.2" %}
{% set AS_version="1.3.1" %}
{% set AA_version="1.4.r1" %}
{% set AC_version="1.1.3" %}

package:
name: {{ name }}
Expand All @@ -11,12 +11,12 @@ source:
# the sha256 sum is generated by doing
# $ wget -O- [URL] | shasum -a 256
- url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz
sha256: 40d3b4560fb2c9fd0cbc5166b9d136751ff16217a6228fb38b74e12207ef5b63
sha256: b74c8201b9e53493a8f1604f6035fa9e42c0ce7d1a258f9095b037afe2d5f2d8
- url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz
sha256: 44466fb4a275f5dd1a142269bb72dc53a651b9d9193e5ba799eee14f0f693f89
sha256: d62e30999c69b994691c8a61b09255a0b223906fd76709febc0ae8387164f208
folder: ampliconarchitectlib
- url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz
sha256: 0f57d0775d7b68a76fab6cc375e45410fe76dd9245697855f257378bd1f21650
sha256: 105f3d0dfd99c52bb8cd988f3fd71afb064b01167a36b72d8fe789f5dfe8c9f5

build:
noarch: python
Expand All @@ -41,12 +41,14 @@ requirements:
- pysam
- samtools
- scipy
- bedtools
host:
- python >=3

test:
commands:
- AmpliconSuite-pipeline.py -v
- GroupedAnalysisAmpSuite.py -v
- amplicon_classifier.py -v
- feature_similarity.py -h
- make_results_table.py -h
Expand Down
6 changes: 3 additions & 3 deletions recipes/anchorwave/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{% set name = "anchorwave" %}
{% set version = "1.2.2" %}
{% set tag = "v1.2.2" %}
{% set sha256 = "db951e2fc8e493ce29e8c6e4f0226a68dc2fdc62631c1fe65077988647e98d01" %}
{% set version = "1.2.3" %}
{% set tag = "v1.2.3" %}
{% set sha256 = "1f689c06f9bbc8e1ed64c0addf4aaf5d172a2fea1e55660b8d3f6dfdffe3f157" %}

package:
name: {{ name }}
Expand Down
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