Update recipe for dysgu #55263
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Update recipe for dysgu #55263
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diekhans
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* Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml
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* Update mirtop to 0.4.30 (#55192) * Update bioframe to 0.8.0 (#55196) * Update palantir to 1.4.0 (#55195) * Update sopa to 2.0.4 (#55194) * Update cgecore to 2.0.1 (#55185) * Update trgt to 2.0.0 (#55193) * Update muat to version 0.1.9 (#55190) Co-authored-by: primasan <primasan@ad.helsinki.fi> * Update Clair3 to v1.1.0 (#55188) * Update polap to 0.4.3.7.5 (#55182) * Update polap to v0.3.7.3 build1 * Update polap to v0.4.3.7 build1 * Update polap to v0.4.3.7 build1 * Update polap to v0.4.3.7 without blast package * Update polap to v0.4.3.7 build1 without dflye * Update polap to v0.4.3.7.1 * Update polap to v0.4.3.7 build1 * Update polap to v0.4.3.7 build1 * Update polap build1 * Update polap build1 * Update polap build1 * Update polap to v0.4.3.7 build1 * Update meta.yaml * Update polap to v0.4.3.7 build1 without cflye * Update polap to v0.4.7.3 not yet * Update polap to v0.4.3.7 * Update polap to v0.4.3.7 build2 * Update polap to v0.4.3.7.2 * Update polap to v0.4.3.7.2 * Update polap to v0.4.3.7.2 * Update polap to v0.4.3.7.3 * Update polap to v0.4.3.7.3 try3 * Update polap to v0.4.3.7.3 try4 * Update polap to v0.4.3.7.3 * Update polap to v0.4.3.7.4 * Update polap to 0.4.3.7.5 --------- Co-authored-by: Sang Chul Choi <sangchulchoi@sungshin.ac.kr> * add statsmodels (#55179) * Update meta.yaml (#55181) * Update phabox to 2.1.11 (#55160) * Update piranha-polio to 1.5.1 (#55158) * Update recipe rsat-core, was blacklisted (#55152) * Updated version of RSAT * Updated conda recipe * updated to 2025-03-26 * add version.txt * removed rsat-core from blacklist * updated documentation and citation * commented out 2 perl deps * modified from Fabian's * removed host section and commented out deps * added missing \ * copy also folder share * added r-base to build: * passes test, complains perl: warning: Setting locale failed * passes tests with bioconda-utils build --docker --mulled-test --packages rsat-core * added LC_ALL * imports perl-postscript-simple, see #55114 * release of 2025.04.04 * rebuild after recipes/rsat-core/meta.yaml * build number reset to 0 after PR lint failure --------- Co-authored-by: Fabián Robledo <fabianry97@gmail.com> * Add v2.1.0 (#55167) * Update GRAMPA recipe (#55163) * update grampa recipe to add tests script * adding missing requirement for tests (unzip) * update link command * making a copy instead of a link since there seems to be a problem with that now * Update s4pred (#55169) * s4pred build version bump to retry creating container * download model weights, move to same folder as python scripts, make bash wrappers in bin folder, update test command run with actual script execution * renamed to run_model to match the python script, changed build number to 1 * added wget to host * Update treesimulator to 0.2.8 (#55037) * Update treesimulator to 0.2.5 * Update treesimulator to 0.2.6 * Update treesimulator to 0.2.7 * Update meta.yaml * Update meta.yaml * Update treesimulator to 0.2.8 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update isescan to 1.7.3 (#55197) * Update clair3-illumina to 1.1.0 (#55198) * Add cawlign recipe (#55168) * initial cawlign recipe * fix cawlign build number * fix cawlign build issues * Add MPRAlib (#55159) * initialization of MPRAlib * typo fix * ? * Add rdrpcatch (#55124) * Add rdrpcatch * fixed requests dependency * fixed run_exports * More clear deps * clean up recipe --------- Co-authored-by: dtriskar <dkarapliafis@gmail.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * install_mimi_1.0.0 (#55161) * install_rotate_1.0 * install_mimi_1.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * Update reduce to 4.15 (#55186) * Update reduce to 4.15 * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update last to 1639 (#55199) * Update resfinder to 4.7.0 (#55177) * Update resfinder to 4.7.0 * Update meta.yaml * revert to git --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * add ovrlpy recipe (#55183) Co-authored-by: niklasmueboe <niklasmueboe@github.com> * Update ncbitax2lin to 2.4.1 (#55201) * Update ncbitax2lin to 2.4.1 * add run_exports --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update kma to 1.5.0 (#55200) * Add mypmfs_py package (#55171) * mypmfs_py package * Update meta.yaml * Update meta.yaml * Update meta.yaml license-family * Update meta.yaml py versions fix * Update meta.yaml pin_compatible * Update meta.yaml lowercase name * Update meta.yaml update requirements * Update meta.yaml dependencies fix * Update meta.yaml c++ dependency and license file fix * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update rdrpcatch to 0.0.3 (#55202) * Update mity to 1.2.0 (#55176) * Update mity to 1.2.0 * clean up recipe --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Add recipe for GCI (#54829) * init gci * lint fixes * author recommendations * update url * Update meta.yaml * Delete recipes/gci/build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update genin2 to 2.1.2 (#54932) * Update genin2 to 2.0.3 * Update genin2 to 2.1.0 * Update genin2 to 2.1.1 * Update genin2 to 2.1.2 * add requests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pymummer to 0.12.0 (#54811) * Update pymummer to 0.12.0 * Update meta.yaml * Update temp_dir_path.patch * Delete recipes/pymummer/temp_dir_path.patch * remove patch --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update fairy to 0.5.8 (#54554) * Update fairy to 0.5.8 * Update meta.yaml * Update build.sh * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update biskit to 3.0.1 (#54543) * Update biskit to 3.0.0 * add run_exports * Update biskit to 3.0.1 * clean up recipe * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update cnvpytor to 1.3.2 (#54515) * Update cnvpytor to 1.3.2 * Update meta.yaml * Update meta.yaml * fix typo * Update and rename post-link.sh to .post-link.sh * Delete recipes/cnvpytor/.post-link.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update survindel2 to 1.1.4 (#54542) * Update survindel2 to 1.1.4 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pastrami to 1.0.0 (#54438) * Update pastrami to 1.0.0 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pybwa to 2.0.1 (#55205) * Update mpralib to 0.6.1 (#55214) * Add r-pio (#55213) * add r-pio * end line * Update r-acidgenomes to 0.7.5 (#55216) * Update zol to 1.5.10 (#55231) * Update ToolDistillator from 0.9.1 to 0.9.2 (#55217) * Update meta.yaml for ToolDistillator 0.9.2 * add setuptools * Update virulencefinder version (#55212) * Update virulencefinder version * RM old code from build.sh * Add pip install to build.sh * Add pdm-backend to meta.yaml * Update nextclade to 3.13.0 (#55240) Co-authored-by: nextstrain-bot <nextstrainbot@nextstrain.org> * Add `wget` to fusioncatcher dependencies (#55242) * Add `wget` to fusioncatcher dependencies * bump build number * Add run_exports * grampa recipe: add build script and update tests script (#55246) * Update kbo-cli to v0.2.1. (#55227) * Update kbo-cli to v0.2.1. * Update url and sha256sum * Update dependencies ganon v2.1.1 (#55248) * fastqtk: add linux-aarch64 (#55209) * fastqtk: add linux-aarch64 * spacing change , to re-start CI * ➕ Update dependencies for vuegen v0.3.2 (#55210) * ➕ Update dependencies for vuegen v0.3.2 * ⬇️ Decreaser build number * ⬆️ Increase build number * ⬆️ Increaser build number bc of circleci error * epa-ng: add linux-aarch64 (#55238) * epa-ng: add linux-aarch64 * add patches to enable aarch64 * New patches - to be applied at build time * use cmake < 4 - this package cannae handle it * - patch the origin of the x86_64 specific genesis code. * progress towards sorting out cxxflags * limit patch to the origin of the arch specific bit * set CXXFLAGS to CMake * pass cxxflags in quotes * no need to double-run make * Add cmake patch * remove cxxflags setting - it's not using them * add patch for CMakeLists.txt * FIX incorrect source for r-scbio (#55229) * FIX incorrect source code After amitfrish/scBio#21: scBio release 0.1.4 has not up-to-date archive assets, resulting in arguments for function CPM() not present in the conda package when they should be present. * Update meta.yaml after failed PR to bioconda-recipes max_pin="x.x.x" was chosen as per https://bioconda.github.io/contributor/linting.html#missing-run-exports and inspection of scBio repo (https://github.com/amitfrish/scBio), breaking change can be introduced even in patch release * Update aliceasm (#55237) * add aliceasm * run_exports in aliceasm recipe * build number * correct linting * added omp for osx * added omp for osx * Update recipes/aliceasm/meta.yaml * added bcalm dependancy * moved to version 0.6.33 * debugged dependencies * solved bug bcalm --help retruns 1 * correct dep * update aliceasm * empty --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update plink2 to 2.0.0-a.6.9 (#55220) * update plink2 to 2.0.0-a.6.9 * reset build number * fix version number to remove hyphen * Update rdrpcatch to 0.0.4 (#55233) * Update captus to 1.3.3 (#55232) * Update hictk to 2.1.1 (#55230) * Updated build for ARM (#55218) * Update ont-modkit to 0.4.4 (#55206) * Update mimeo to 1.2.1 (#55207) * Update libcifpp to 8.0.0 (#55208) * Update resfinder to 4.7.2 (#55211) * Update resfinder to 4.7.1 * Update resfinder to 4.7.2 * Update tower-cli to 0.11.2 (#55243) * Update snakemake-executor-plugin-slurm to 1.2.0 (#55219) * Update tiddit to 3.9.3 (#55221) * Update pyjess to 0.5.0 (#55222) * Update fasten to 0.8.7 (#55228) * Update kaptive to 3.1.0 (#55234) * Update pybiolib to 1.2.701 (#55235) * Update architeuthis to 0.4.0 (#55236) * Update picrust2 to 2.6.2 (#55239) * Update ppanggolin to 2.2.2 (#55249) * Update sawfish to 1.0.0 (#55250) * Update severus to 1.5 (#55251) * Add amulety recipe (#55258) * Add epicore recipe (#54954) * add recipe for epicore package * add run_exports * update meta.yaml * remove outdated meta.yaml * move meta.yaml * update script command * update version * update sha256 --------- Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> * Update augur to 29.1.0 (#55256) * Add cvanmf recipe (#55262) * Update strobealign to 0.16.0 (#55270) * Update lexicmap to 0.7.0 (#55271) * Update nanomotif to 0.6.0 (#55264) * Update screadcounts to 1.4.1 (#55275) * Update screadcounts to 1.4.1 * Update meta.yaml --------- Co-authored-by: Nathan Edwards <edwardsnj@users.noreply.github.com> * Update giatools to 0.4.0 (#55281) * Add eider recipe (#55279) * Update oarfish to 0.8.0 (#55289) * Update screadcounts to 1.4.2 (#55290) * Update whatshap to 2.6 (#55280) * Update r-acidbase to 0.7.4 (#55303) * Update latch to 2.59.0 (#55286) * Update argnorm to 0.8.0 (#55306) * Update quantms-rescoring to 0.0.8 (#55312) * Update r-acidsinglecell to 0.4.4 (#55304) * Update metafun to 0.3.0 (#55310) * Update metafun to 0.3.0 * Update metafun to 0.3.0 * reduce: Update build script to add `-DHET_DICTIONARY` and `-DHET_DICTOLD` flags (#55300) * reduce: Update build script to add `-DHET_DICTIONARY` and `-DHET_DICTOLD` flags * reduce: Add comment referencing issue for `-DHET_DICTIONARY` and `-DHET_DICTOLD` flags * Update to v4.5 (#55299) * Update to v4.5 * Update meta.yaml v4.5 * Install mimi 1.0.0 (#55288) * install_rotate_1.0 * install_mimi_1.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * Update meta.yaml * setuptools is needed after all * install_mimi_1.0.1 * install_mimi_1.0.1 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update bindash to 2.4 (#55292) * Update bindash to 2.4 * Update bindash to 2.4 * Update plothic to 1.0.0 (#55307) * Update ampliconsuite to 1.3.6 (#55298) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update Sentieon recipe to 202503 (#55295) * Update carveme to 1.6.3 (#55265) * Update captus to 1.3.4 (#55259) * Update bedops to 2.4.42 (#55254) * Update recipe for dysgu (#55263) * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Add tmscoring (#55261) * add yaml * python <3.12 * make it noarch * Update perl-math-bigint to 2.005003 (#55316) * Update reframed to 1.5.4 (#55266) * Update reframed to 1.5.4 * add setuptools --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snakemake-executor-plugin-slurm to 1.2.1 (#55285) * Update snakemake to 9.1.10 (#55276) * Update picard to 3.4.0 (#55314) * Update picard-slim to 3.4.0 (#55313) * Update scanpy-cli to 0.2.0 (#55305) * Update scanpy-cli to 0.1.7 * Update scanpy-cli to 0.1.8 * Update scanpy-cli to 0.2.0 * Update oakvar to 2.12.12 (#55297) * Update solvebio to 2.30.1 (#55282) * Update drep to 3.6.1 (#55294) * Update drep to 3.6.1 * add setuptools * add networkx --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update shiba2sashimi to 0.1.4 (#55319) * Update kmercamel to 2.1.1 (#55317) * Update kmercamel to 2.1.1 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update cenote-taker3 to 3.4.0 (#55273) * Update cenote-taker3 to 3.4.0 * pin pyhmmer to >=0.11.0 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update igv to 2.19.3 (#55296) * Update igv to 2.19.3 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update srnaMapper to new version (#55241) * Update srnaMapper to new version * Explicitely add BWA * Reset build number to 0 * Correct lib path * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Updating build of arborator (#55278) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add mimick recipe (#55284) * add mimick recipe * fix the folder error * rm skip * fix biopython bound * fix all bounds :( * rm aarch64 b/c of incompatibility with pywgsim * pin python to >=3.10 according to pyproject.toml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Removed wfa2 external dependency in linux (#55277) * Removed wfa2 external dependency in linux * Update build.sh * Fix ARM build * trigger GitHub actions * trigger GitHub actions * Update build.sh * clean up recipe * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update r-geneexpressionfromgeo to 1.2 (#55267) * Update r-geneexpressionfromgeo to 1.2 * add run_exports * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update floria to 0.0.2 (#55255) * Update floria to 0.0.2 * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * eskrim does not work with python 3.13 (#55269) * eskrim does not work with python 3.13 * clean up recipe --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update perl-test-file to 1.995 (#55321) * Update odgi to 0.9.1 (#55252) * Update odgi to 0.9.1 * Fix cmake command to include policy version for build consistency * Fix cmake command by removing redundant policy version specification * Fix cmake command by moving policy version specification to the correct position * Update meta.yaml * Update build.sh --------- Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update searchgui to 4.3.14 (#55322) * Update fusionreport to 4.0.0 (#55215) * update fusionreport * apply linitng * apply linting * clean up recipe * fix typo * fix source URL --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update smoothxg to 0.8.1 (#55253) * Update smoothxg to 0.8.1 * Add CMAKE_POLICY_VERSION_MINIMUM to cmake commands in build.sh * Remove redundant CMake policy version specification in build command * Fix cmake command formatting in build.sh * Update meta.yaml * Update build.sh * Update build.sh * fix typo * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml --------- Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update captus to 1.3.6 (#55320) * Update captus to 1.3.5 * add entry_points * Update build.sh * Update meta.yaml * Delete recipes/captus/build.sh * Update meta.yaml * Update captus to 1.3.6 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update aviary to 0.12.0 (#55323) * Update aviary to 0.12.0 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update mypmfs_py to 0.1.8 (#55225) * Update mypmfs_py to 0.1.8 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * xtandem: add arm64 build (#55324) * tandemx: add arm64 build * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Add dmox (#54435) * Create meta.yaml This is the framework for the conda recipe for dmox. Once a release is tagged, we can submit this PR to bioconda for testing @iago-lito * Update meta.yaml remove the skip option * Update meta.yaml * adjust installation to move binary to PATH * add checksum * add proper parameters as specified by linter * rm host section, add noarch skip * align with current rust compiling recipe guide * add AT symbol to reciple maintainer * rm AT sign * add "v" to url * add cmake * just add cxx compiler * make sure cmake is a dep * just C compiler, not cxx? * Attempt to fix zlib-ng build. * Add cargo to test dependencies. * Move `cargo test` to build stage. * Leave tombstone into test section. * Replace tombstone with `dmox --help`. * Introduce and check third-party licenses. * Add THIRDPARTY.yml to license-file. * Attempt to fix MACOS build. * 🐛 Attempt to debug macos build. * clean up recipe * fix typo * Update build.sh --------- Co-authored-by: Iago Bonnici <iago.bonnici@umontpellier.fr> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add MACH2 v1.0.1 (#54261) * Add MACH2 v1.0.1 * Add MACH2 v1.0.1 - mentioned gurobi channel * Add MACH2 v1.0.1 - changed gurobipy to gurobi * Add MACH2 v1.0.1 - made gurobi optional in code * Update sawfish to 1.0.1 (#55326) * Update gapmm2 to 25.4.13 (#55328) * Add qcatch 0.1.2 to bioconda (#55074) * Add qcatch 0.1.2 to bioconda * clean up recipe * add requests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update cogent3 to 2025.3.22a4 (#54902) * Update cogent3 to 2025.3.22a3 * Update cogent3 to 2025.3.22a4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update captus to 1.3.7 (#55330) * Update teloscope to 0.1.0 (#55329) * Update teloscope to 0.1.0 * Update meta.yaml * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update gsearch v0.2.6 (#55325) * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Rebuild gmap (#55331) * Update carveme to 1.6.4 (#55332) * Rebuild libcifpp (#55334) * Update checkqc to 4.0.6 (#55335) * Update checkqc to 4.0.6 * Add jsonschema * Update checkqc to 4.0.6 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update PPanGGOLiN (#55260) * update ppanggolin recipe * add space between tool and version * add space between tool and version again * Update ltr_harvest_parallel (#55283) * change ltr_harvest_parallel repo source * fix duplicate key * osx-arm64 build for bioconductor-rhtslib and bioconductor-rsamtools (#55351) * osx-arm64 build for bioconductor-rhtslib and bioconductor-rsamtools * bump build number * Update methylartist to 1.4.0 (#55344) * Update methylartist to 1.4.0 * add setuptools --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update wfmash to 0.23.0 (#55353) * Update pggb to 0.7.3 (#55345) * Update pggb to 0.7.3 * update versions * Update vg dependency version to 1.63.1 * Update wfmash dependency version to 0.14.0 --------- Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> * add osx-arm64, bump build number (#55354) * Update arvados-python-client to 3.1.1 (#55350) * Update ebi-eva-common-pyutils to 0.7.0 (#55338) * Update sniffles to 2.6.2 (#55337) * Update sniffles to 2.6.2 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update ogtfinder to 0.0.2 (#55336) * Update sr2silo to 0.1.1 (#55333) * Update sr2silo to 0.1.0 * add poetry-dynamic-versioning * Update meta.yaml * Update sr2silo to 0.1.1 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * osx-arm64 for bioconductor-sparsearray and bioconductor-s4arrays (#55356) * Update latch to 2.59.1 (#55360) * Update qcatch to 0.2.3 (#55359) * Update snakemake to 9.1.11 (#55341) * Update fast2q to 2.7.8 (#55348) * Update fast2q to 2.7.8 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add DeepDETAILS (#55349) * Update captus to 1.3.8 (#55362) * Update drep to 3.6.2 (#55352) * Update drep to 3.6.2 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * hictkpy: bump to v1.2.0 (#55339) * Simplify recipe * Bump hictkpy * Bugfix * Update URL * Remove Python version constraints from `vambcore` (#55272) * Remove Python version constraints from `vambcore` * Remove cross-compilation * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snakemake to 9.2.0 (#55361) * Add TWILIGHT v0.1.1 (#55203) * add twilight * add space between package and version * add pin * modify package name * Update meta.yaml * Update build.sh --------- Co-authored-by: y3tseng <y3tseng@AD.UCSD.EDU@raptor.ucsd.edu> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipe for bbmapy (#55204) * Add recipe for bbmapy - a low dependency bbmap python wrapper * fix recipe for bbmapy * fix recipe after removing pytools from bbmapy * updating bbmapy version * move ensure_java to test on run, not build * fix wrong function name * add beefy Xmx to test commands * change ensure java function * change ensure java to use conda_prefix (again?) * fix tests - ensure_java moved * clean up recipe * revert license_file --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update cleanifier to 0.2.1 (#54925) * Update cleanifier to 0.2.1 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update Vamb to 5.0.3 (#54983) * Update Vamb to 5.0.2 * Add identifiers * Relax version requirements * Update requirements * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update mimick to 1.0.1 (#55370) * Update captus to 1.3.9 (#55364) * Update captus to 1.3.9 * fix install script --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update dbcan to v5.0.3 (#55369) * Add mpboot (#55008) * Add mpboot * fix sha * Try adding minimum cmake version arg * fix make command * fix make * tryagain * Try patching * unix2dos * try again * Fix exe nameTry again * simplify, use zlib>1.3.1 * fix * Try againtry again * fix copy * f * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update muat to version 0.1.10 (#55365) Co-authored-by: primasan <primasan@ad.helsinki.fi> * Add bakrep-cli to BioConda (#54922) * Create meta.yaml * add run_exports to meta.yaml * fix package in run_exports * change subpackage name to bakrep-cli in meta.yaml * add setuptools --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update mysterymaster meta.yaml (#55347) * Add cdskit (#55257) * Add cdskit recipe * Add cdskit recipe (fixed submodule issue) * Trigger build by bumping build number * Fix source URL and sha256 * Fix sha256 for cdskit source tarball * Fix: remove duplicate build script definition * Fix: meta.yaml license * Add Bioconda recipe for cdskit v0.14.1 * Add Bioconda recipe for cdskit 0.14.1 * Fix lint: reset build number and add run_exports * Fix: requirements python version * rmblast: add osx-arm64 (#55363) * rmblast: add osx-arm64 * Clean up rmblast * add zstd * Update build.sh --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add kmer2stats recipe (#55224) * Add kmer2stats recipe * fix typo * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * fix test, did a little mistake * fix test * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update dnachisel to 3.2.15 (#55068) * Update gsmap to 1.73.0 (#53896) * add r-bpcells (#55118) * add r-bpcells * adjust deps * libs * libs * license name * libs * patch libhwy config * full patch * fix patch * raw test again * macs2 test * use vendor libhwy on osx * skip non-linux * comment unit test failures * add granges conversion patch * test against macs3 * Update genmod to 3.10.1 (#55372) * Update pasta (#54563) Co-authored-by: ZerryNi <996002763.com> Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> * add osx builds for rtracklayer, genomicalignments (#55357) * add osx builds fr rtracklayer, genomicalignments * add osx-arm64 & bump build for r-restfulr * Update wally to 0.7.1 (#55380) * add osx-arm64 for bioconductor-deseq2 (#55382) * add osx-arm64 for bioconductor-deseq2 * reset build number * retry bumping build number * Update quantms-rescoring to 0.0.9 (#55391) * Build raxml-ng for osx-arm64 (#55381) * Build raxml-ng for osx-arm64 * bump build number of course * Set cmake minimum to 3.5 * Update nanomotif to 0.6.1 (#55377) * Update cmat to 3.3.3 (#55383) * Add ervmancer (#55385) * init ervmancer bioconda package for PR * update with run_export * chore: update versions for dependencies, update summary and description of package * chore: fix spacing for python deps * chore: fix spacing for all deps * chore: fix phrasing for description/summary * remove channels block * Update psm-utils to 1.4.1 (#55389) * Update pilea to 0.2.1 (#55393) * Update ms2rescore to 3.1.5 (#55387) * Update biscuit to 1.6.1.20250415 (#55394) * Update buscolite to 25.4.3 (#55371) * Update buscolite to 25.4.3 * add packaging --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update augur to 30.0.0 (#55395) * sfld: add linux-aarch64 (#55392) * paraclu: add linux-aarch64 (#55384) * paraclu: add linux-aarch64 * Update meta.yaml: remove whitespace to trigger build; last build was borked by transient net error * add osx-arm64 * Update gottcha2 to 2.1.9 (#55396) * Add r-floral (#55132) * Add r-floral * r-floral lint fixes * r-floral lint fixes * fix r-floral * Update recipes/r-floral/meta.yaml Co-authored-by: Mervin Fansler <mmfansler@gmail.com> * Apply suggestions from code review Co-authored-by: Mervin Fansler <mmfansler@gmail.com> * Add missing dependencies for r-floral --------- Co-authored-by: Mervin Fansler <mmfansler@gmail.com> * Update r-classdiscovery to 3.4.8 (#55165) * Update r-classdiscovery to 3.4.8 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update Replidec v0.3.4 (#55375) * replidec_v0.3.4 * add run_export * UPDATE:replidec_v0.3.4 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update ampd-up to 1.0.1 (#55397) * delly: add arm64 build (#55398) * add htslib to the run deps (#55388) * Rebuild postmaster recipe (#55400) * Rebuild postmaster recipe * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update msoma to 0.1.1 (#55404) * cdbtools: bump build to with fresher zlib (#55399) * cdbtools: bump build to wih fresher zlib * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * clean up recipe --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update dna_features_viewer to 3.1.4 (#55017) * Update dna_features_viewer to 3.1.4 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * update concoct (#54560) * concoct * Update meta.yaml * Update build.sh --------- Co-authored-by: ZerryNi <996002763.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update annotsv to 3.4.6 (#54194) * Update annotsv to 3.4.5 * Update annotsv to 3.4.5 * Update annotsv to 3.4.6 * edit tests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update instanovo to 1.1.1 (#54966) * Update instanovo to 1.1.0 * Update instanovo to 1.1.1 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update flair to 2.1.2 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pneumo-typer to v2.0.1#2 (#55406) * Update gcluster to v2.0.7#4 (#55405) * Rebuild lastz recipe (#55410) * Rebuild lastz recipe * Update build.sh * Update caspeak to 1.1.2 (#55411) * Relax Python version requirement to >=3.8 (support Python 3.12) (#55407) * Relax Python version requirement to >=3.8 (support Python 3.12) * Bump build number to 1 for Python 3.12 support * Update sha256 for rebuilt 0.14.2 * Fix sha256 for cdskit 0.14.2 * Fix source URL and sha256 for cdskit v0.14.2 (kfuku52) * Trigger rebuild after upstream fix * Fix source URL and sha256 for cdskit v0.14.2 (kfuku52) * update pigpen_0.0.6 to include r-lme4 and postmaster (#54546) * update pigpen_0.0.6 to include r-lme4 and postmaster * increment build number * postmaster not available for osx * postmaster not available on aarch64 * Update recipes/pigpen/meta.yaml Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> * Update meta.yaml --------- Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipes panaln (#55414) * Create meta.yaml * Create build.sh * Update tower-cli to 0.11.3 (#55416) * Update snakemake to 9.3.0 (#55417) * augustus: add linux-aarch64 (#55413) * augustus: add linux-aarch64 * Create conda_build_config.yaml: pin due to cstdint declaration requirement * aster: add arm64 build (#55415) * aster: add arm64 build * Update build.sh * Update atlas to 2.0.0-rc.10 (#55378) * update to version 10 * for some reason, mkl seems to be needed now * Update fastp to 0.24.1 (#55418) * Update muat to version 0.1.11 (#55420) Co-authored-by: primasan <primasan@ad.helsinki.fi> * Update roadies to 0.1.8 (#53044) * update roadies * updated build files to add correct perl version * fixed package name * updated meta.yaml * fixed mashtree dependencies * added gcc * added c compiler * added gcc to run and host * fix for gcc not working * fix in build file for gcc not working * updated lastz flags * removed conda_build_config file * updated lastz * updated lastz gcc not found error * updated lastz to take current master - temporary fix * updated with new LASTZ release * Update meta.yaml * removed redundant line of code * Update build.sh * Update meta.yaml * add lastz * pin lastz to >=1.04.52 Co-authored-by: M Bernt <m.bernt@ufz.de> * delete extraneous section now that lastz is built with _40 Co-authored-by: M Bernt <m.bernt@ufz.de> * Update build.sh * add aster --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: M Bernt <m.bernt@ufz.de> * Update mehari to 0.35.0 (#53131) * Update mehari to 0.35.0 --------- Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de> Co-authored-by: Till Hartmann <till.hartmann@udo.edu> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update annonars to 0.44.0 (#53114) * Update annonars to 0.44.0 * update recipe meta.yaml --------- Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de> * Update grz-cli to 0.4.0 (#55427) --------- Co-authored-by: Travis Wrightsman <travis@wrightsman.org> * feat: primer3 to support osx-arm64 (#55432) * Update ncbi-stxtyper to 1.0.42 (#55436) * Update r-ukbrapr to 0.3.5 (#55430) * Update captus to 1.4.0 (#55433) * Update roadies to 0.1.10 (#55431) --------- Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Co-authored-by: Prima Sanjaya <mr.primasanjaya@gmail.com> Co-authored-by: primasan <primasan@ad.helsinki.fi> Co-authored-by: zhenxian <920596906@qq.com> Co-authored-by: Sang Chul Choi <goshng@yahoo.co.kr> Co-authored-by: Sang Chul Choi <sangchulchoi@sungshin.ac.kr> Co-authored-by: Xi Chen <38089207+xinehc@users.noreply.github.com> Co-authored-by: Kez Cleal <42997789+kcleal@users.noreply.github.com> Co-authored-by: eead-csic-compbio <bcontreras@eead.csic.es> Co-authored-by: Fabián Robledo <fabianry97@gmail.com> Co-authored-by: Roberto Rossini <71787608+robomics@users.noreply.github.com> Co-authored-by: Gregg Thomas <gwct@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Danielle Callan <53306535+d-callan@users.noreply.github.com> Co-authored-by: Max <visze@users.noreply.github.com> Co-authored-by: dimitris-karapliafis <116268242+dimitris-karapliafis@users.noreply.github.com> Co-authored-by: dtriskar <dkarapliafis@gmail.com> Co-authored-by: Nabil Rahiman <nabil.rahiman@gmail.com> Co-authored-by: niklasmueboe <42138117+niklasmueboe@users.noreply.github.com> Co-authored-by: niklasmueboe <niklasmueboe@github.com> Co-authored-by: alexhold5 <87720137+alexhold5@users.noreply.github.com> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Moray Smith <65286772+SwiftSeal@users.noreply.github.com> Co-authored-by: Brandon Hastings <65084955+brandon-hastings@users.noreply.github.com> Co-authored-by: Clea Siguret <37694850+clsiguret@users.noreply.github.com> Co-authored-by: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Co-authored-by: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Co-authored-by: nextstrain-bot <nextstrainbot@nextstrain.org> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Tommi Mäklin <tommi@maklin.fi> Co-authored-by: pirovc <4673375+pirovc@users.noreply.github.com> Co-authored-by: David Lecomber <david.lecomber@arm.com> Co-authored-by: Sebastián Ayala Ruano <52267585+sayalaruano@users.noreply.github.com> Co-authored-by: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com> Co-authored-by: RolandFaure <64131971+RolandFaure@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Hugo Tavares <tavareshugo@users.noreply.github.com> Co-authored-by: Vivaswat Shastry <vivshastry@gmail.com> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Jana Hoffmann <105642758+janaHoffmann1@users.noreply.github.com> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Anthony Duncan <36088426+apduncan@users.noreply.github.com> Co-authored-by: Nathan Edwards <edwardsnj@users.noreply.github.com> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: UENO, M. <eunosium-1128@live.jp> Co-authored-by: Ryan Doughty <57912116+rdoughty10@users.noreply.github.com> Co-authored-by: Jens Luebeck <jluebeck@ucsd.edu> Co-authored-by: Don Freed <DonFreed@users.noreply.github.com> Co-authored-by: Rubén Chaves <ruben.chaves@irbbarcelona.org> Co-authored-by: mzytnicki <34034101+mzytnicki@users.noreply.github.com> Co-authored-by: Aaron Petkau <aaron.petkau@gmail.com> Co-authored-by: Pavel V. Dimens <19176506+pdimens@users.noreply.github.com> Co-authored-by: Michael Kovaliov <32510658+RedPenguin100@users.noreply.github.com> Co-authored-by: Florian Plaza Oñate <4588656+fplazaonate@users.noreply.github.com> Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> Co-authored-by: Iago Bonnici <iago.bonnici@umontpellier.fr> Co-authored-by: Mrinmoy Saha Roddur <mrinmoy.roddur@gmail.com> Co-authored-by: Yuan Gao <107954058+ygao61@users.noreply.github.com> Co-authored-by: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Co-authored-by: Jean Mainguy <jean.mainguy@outlook.fr> Co-authored-by: Jacques Dainat <jacques.dainat@gmail.com> Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com> Co-authored-by: Apratim Mitra <16709900+mitraak@users.noreply.github.com> Co-authored-by: Li Yao <ly349@cornell.edu> Co-authored-by: Antônio Camargo <apcamargo@users.noreply.github.com> Co-authored-by: y3tseng <146570926+y3tseng@users.noreply.github.com> Co-authored-by: y3tseng <y3tseng@AD.UCSD.EDU@raptor.ucsd.edu> Co-authored-by: UriNeri <41674327+UriNeri@users.noreply.github.com> Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com> Co-authored-by: Oliver Schwengers <oliver.schwengers@computational.bio.uni-giessen.de> Co-authored-by: grabherr <manfredgrabherr@gmail.com> Co-authored-by: Asaka Yusuke <48976189+kamome1201@users.noreply.github.com> Co-authored-by: Adam Taranto <adam.p.taranto@gmail.com> Co-authored-by: SantaMcCloud <100047964+SantaMcCloud@users.noreply.github.com> Co-authored-by: Mervin Fansler <mervin.fansler@bric.ku.dk> Co-authored-by: ZerryNi <47553636+ZerryNi@users.noreply.github.com> Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> Co-authored-by: Bryant Duong <bryantduong@users.noreply.github.com> Co-authored-by: Tyler Funnell <tfunnell@coh.org> Co-authored-by: Mervin Fansler <mmfansler@gmail.com> Co-authored-by: pengSherryYel <32877803+pengSherryYel@users.noreply.github.com> Co-authored-by: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Co-authored-by: Matthew Taliaferro <taliaferrojm@gmail.com> Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> Co-authored-by: Guo3 <jgxygll@163.com> Co-authored-by: David Lecomber <david+dslarm@lecomber.net> Co-authored-by: Andreas Füglistaler <andreas.fueglistaler@protonmail.com> Co-authored-by: Anshu Gupta <114828525+ang037@users.noreply.github.com> Co-authored-by: M Bernt <m.bernt@ufz.de> Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de> Co-authored-by: Till Hartmann <till.hartmann@udo.edu> Co-authored-by: Travis Wrightsman <travis@wrightsman.org> Co-authored-by: Nils Homer <nh13@users.noreply.github.com>
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Adds
- osx-arm64