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feat: add initial support for arm builds #40550
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b141b9c
Update koverage to 0.1.11 (#45697)
BiocondaBot 87bdc09
Update trimnami to 0.1.3 (#45698)
BiocondaBot 04a385c
Update nanomotif to 0.1.17 (#45699)
BiocondaBot 4445fa1
Add git to resfinder (#45686)
ryanjameskennedy 8d6f2a7
Add Scevan R package recipe (#45649)
fc9275a
Update orsum (#45701)
ozanozisik a185699
Add ntsynt (#45692)
lcoombe e9d741f
Update pango-designation to 1.25 (#45717)
BiocondaBot ed8e632
Update planemo to 0.75.21 (#45713)
BiocondaBot a3dcc9c
Update annonars to 0.35.0 (#45712)
BiocondaBot b91f4ac
Update cramino to 0.14.1 (#45710)
BiocondaBot 13394e5
Update vcfsim to 1.0.9.alpha (#45719)
BiocondaBot 389f9e1
Update dfast to 1.2.21 (#45702)
BiocondaBot 4eafef2
Update oakvar to 2.9.87 (#45696)
BiocondaBot d8eae6f
Fix pydantic dependency of varfish-cli more strictly. (#45703)
holtgrewe 27e54d9
Update assemblycomparator2 to 2.5.18 (#45706)
BiocondaBot 7e01903
Update centrifuger to 1.0.1 (#45711)
BiocondaBot edbc6a8
Update igv-reports to 1.12.0 (#45720)
BiocondaBot 952ae21
Update ndex2 to 3.8.0 (#45721)
BiocondaBot 5143486
Add seqnado (#45705)
CChahrour 98fa66e
Update pangu to 0.2.4 (#45496)
BiocondaBot 61438c4
Update htsinfer (#45633)
balajtimate e719b53
Patch hmftools-sv-prep 1.2.3 (#45694)
scwatts df056b7
Update sepp (#44721)
sjanssen2 b03b752
Update r-jackstraw to 1.3.9 (#45683)
BiocondaBot 6361b1e
Re-points LD_LIBRARY_PATH to dynamically linked library when loading …
adamrtalbot b31d260
Add taxor (#45392)
JensUweUlrich fbc456e
Add recipe for gffpandas v1.2.2 (#45724)
mencian 6faeb4d
Update liftover to 1.1.18 (#45723)
BiocondaBot f1a1021
Update purge_haplotigs to 1.1.3 (#45726)
beardymcjohnface 619e346
Update taxonomy to 0.10.0 (#45674)
mencian 231ac53
Update hecatomb to 1.3.2 (#45729)
BiocondaBot fc8475f
Update primer3-py to 2.0.2 (#45738)
BiocondaBot 2cfa2ba
Update auspice to 2.52.0 (#45745)
joverlee521 f204d2a
Update evofr to 0.1.22 (#45744)
joverlee521 f35c61b
Update aletsch to 1.1.1 (#45736)
BiocondaBot e0c01e2
update verkko to v2.0 (#45708)
skoren 1326a94
Update snakemake to 8.4.8 (#45739)
BiocondaBot 67974cb
Update trgt to 0.8.0 (#45740)
BiocondaBot 662b3f6
Add hmftools-mark-dups 1.1 (#45728)
scwatts 1e5cb52
Add r-linxreport 1.0.0 (#45727)
scwatts 7599d49
Update freyja to 1.4.9 (#45742)
BiocondaBot e3417bf
require python >=3.9 for varfish-cli (#45731)
holtgrewe 066a5a6
Update pymzml to 2.5.4 (#45735)
BiocondaBot 9c38600
Update nanomotif to 0.1.18 (#45734)
BiocondaBot fbe2feb
Update tissuumaps to 3.2.0.4 (#45733)
BiocondaBot 4a1fb37
Add recipe pytransaln v0.2.1 (#45732)
kbseah ddefda8
Update mehari to 0.22.0 (#45730)
BiocondaBot a06525b
Add new graph embedding software for large-scale biological network (…
jianshu93 ed91eb2
Add hmftools-cuppa 1.8.1 (#45643)
scwatts cce88a3
Add recipes for `bigtools` and `pybigtools` (#45634)
jackh726 efe8e26
Update linearpartition to 1.0.1.dev20240123 (#45593)
marcom 1047d93
Add recipe for MultiRNAFold v2.1 (#45623)
marcom 95f8c62
Add MSFragger recipe. (#45127)
reid-wagner 441c1c7
Update arcas-hla to 0.6.0 (#45718)
abuendia ca684bf
Update phykit to 1.13.1 (#45747)
BiocondaBot 8ac2e92
Update scanpy-scripts to scanpy 1.9.x (#45750)
pcm32 40bb118
Update sourmash to 4.8.6 (#45749)
BiocondaBot 8b5a043
Update bx-python to 0.11.0 (#45748)
BiocondaBot e86fca3
Update hmftools-bam-tools 1.2 recipe (#45754)
scwatts eea5269
Update hmftools-sage 3.4 recipe (#45755)
scwatts 3370e7f
Bump GATK4 gcnvkernel (#45759)
matthdsm 7bd086e
Update pymzml to 2.5.5 (#45761)
BiocondaBot 971c7c2
Update bigtools to 0.4.2 (#45756)
BiocondaBot a34fec3
Update GATK4 to 4.5.0.0 (#45762)
matthdsm 02d3b39
Add RecGraph (#45680)
yp 4cf79cd
Add pass (#45722)
lcoombe 44c4beb
MultiQC 1.20 (#45764)
vladsavelyev 43b0720
Update thapbi-pict to 1.0.9 (#45767)
BiocondaBot 1fdaa26
Update ska2 to 0.3.6 (#45768)
BiocondaBot 4d068c8
Update integron_finder to 2.0.3 (#45766)
BiocondaBot 301ddb5
Update assembly_finder to 0.4.2 (#45765)
BiocondaBot 642afc8
Update Lisa2 (#45753)
AllenWLynch 75e0c86
Update mira-multiome to 2.1.1 (#45763)
BiocondaBot 3000ab7
Update samestr to 1.2024.2.post1 (#45737)
BiocondaBot 973a75e
Update augur to 24.2.0 (#45771)
BiocondaBot 810e694
Update ontime to 0.3.1 (#45773)
BiocondaBot c4269e6
Update nextclade to 3.2.0 (#45777)
nextstrain-bot 067edb8
Update clipkit to 2.2.0 (#45774)
BiocondaBot 1f21b25
Update dajin2 to 0.4.1 (#45776)
BiocondaBot 417664e
Update earlgrey to 4.0.8 (#45781)
BiocondaBot 9920006
recipe for segalign-full (#45783)
richard-burhans 95840d0
Update: sepp subrecipe 4.3.10 (#44540)
sjanssen2 9c7399e
Update ncbi-datasets-pylib to 16.4.7 (#45782)
BiocondaBot 33c9d96
Update dxpy to 0.369.1 (#45785)
BiocondaBot a11065f
Update panaroo to 1.4.0 (#45786)
BiocondaBot 570e861
Update meta.yaml (#45769)
mtisza1 34f650f
Add LTR_FINDER_parallel (#45772)
GallVp 72afa88
Update serotypefinder to v2.0.2 (#45770)
ryanjameskennedy 7854fe9
Update Integron finder to new release 2.0.3 (#45778)
bneron 68b1d89
Update infernal to 1.1.5 (#45787)
mencian de77ef7
Update augur to 24.2.1 (#45788)
BiocondaBot 7fa2edb
Update submission-excel2xml to 2.6 (#45789)
BiocondaBot d758b80
Update antismash to 7.1.0 (#45331)
mencian 2cb33b9
Update pangolin-data to 1.25 (#45791)
BiocondaBot bee25d6
Update metacerberus to 1.2.1 (#45790)
BiocondaBot 8085b6a
Update riassigner to 0.4.0 (#45779)
BiocondaBot 438e424
MultiQC: pin plotly version (#45780)
vladsavelyev 24a112f
Update pybiolib to 1.1.1747 (#45800)
BiocondaBot ad40e0a
Update hiphase to 1.4.0 (#45804)
BiocondaBot c9d162c
Update biocommons.seqrepo to 0.6.7 (#45803)
BiocondaBot d922222
Update ena-webin-cli to 7.0.1 (#45802)
BiocondaBot eb8f485
Update pyteomics to 4.7.1 (#45801)
BiocondaBot 4e9bc0c
Update savana to 1.0.5 (#45796)
BiocondaBot 87d0796
Update hmftools-bam-tools to 1.2.1 (#45805)
BiocondaBot 4ec92e1
Update umi_tools to 1.1.5 (#45795)
BiocondaBot 90e15f0
Update pangolin-data to 1.25.1 (#45806)
BiocondaBot 919e57f
Update hicstuff to 3.2.2 (#45811)
BiocondaBot bc8d25e
Update defense-finder to 1.2.1 (#45817)
BiocondaBot 4a76e87
Update terrace to 1.1.2 (#45818)
BiocondaBot 5ff3914
Update snakemake-executor-plugin-slurm to 0.3.1 (#45797)
BiocondaBot ba52aa3
Update snakemake-interface-common to 1.16.0 (#45798)
BiocondaBot 89ae2e1
Update harpy to 0.5.0 (#45714)
pdimens c78943b
Update amdirt to 1.5.0 (#45813)
BiocondaBot 49a3570
Update sercol to 1.0.0 (#45792)
BiocondaBot 4b1ca13
Update snakemake-executor-plugin-googlebatch to 0.3.0 (#45819)
BiocondaBot 63fff9d
Update snakemake-storage-plugin-s3 to 0.2.9 (#45820)
BiocondaBot d902bcb
Add recipe for biodigest (#45751)
lspindler2509 5198536
Add recipe for genbank v0.110 (#45822)
mencian 2e94720
Update peptide-shaker to 3.0.6 (#45823)
mencian 9a6510f
Update phanotate to 1.6.4 (#45809)
BiocondaBot 3b66f2c
Update primer3-py to 2.0.3 (#45825)
BiocondaBot f814437
Update searchgui to 4.3.6 (#45824)
mencian 4b820c0
Update pbsim3 to 3.0.2 (#45827)
BiocondaBot 9100aaa
Update insilicoseq to 2.0.0 (#45816)
BiocondaBot 7160ca0
Update badread to 0.4.1 (#45826)
BiocondaBot 4f01bc3
Update bigscape to 1.1.9 (#45829)
BiocondaBot 2f2123f
Update pyhmmer to 0.10.5 (#45833)
BiocondaBot b79ebf9
Update deeplcretrainer to 0.2.11 (#45831)
BiocondaBot dec0eff
Update ucsc-cell-browser to 1.2.5 (#45841)
BiocondaBot 0717980
Update icescreen v1.3.2 (#45839)
thomas-lacroix 6fd6397
Update ncbi-datasets-pylib to 16.4.8 (#45838)
BiocondaBot 19541a6
fix: pin gffutils python to <3.12 (#45828)
dlaehnemann 5650967
Update bigscape to 1.1.9 (#45836)
SantaMcCloud f4885c4
Update/fix kb-python (#45808)
gennadyFauna 181debb
Add git to serotypefinder (#45837)
ryanjameskennedy 7c56552
Update harpy build to use smaller release instead of source (#45843)
pdimens e30e1bf
added recipe for tracegroomer (#45814)
hechth 7d9d210
Update viralmsa to 1.1.44 (#45850)
BiocondaBot b17aa7e
Update nextclade to 3.2.1 (#45853)
nextstrain-bot c523a23
Update harpy to 0.6.0 (#45844)
BiocondaBot a877805
Create build.sh (#45849)
rob-p fe57e51
Update ganon to 2.1.0 (#45760)
pirovc f5b9c3a
Update tsebra to 1.1.2.3 (#45854)
BiocondaBot 3953434
Update braker3 to 3.0.8 (#45856)
BiocondaBot 39be0b4
Update f5c to 1.4 (#45857)
BiocondaBot c16bfb1
add piscem-infer (#45852)
rob-p 6d3c7e0
Update tracegroomer to 0.1.2 (#45848)
BiocondaBot 394e8ce
Update augur to 24.2.2 (#45847)
BiocondaBot 07816aa
Update snakemake to 8.4.9 (#45858)
BiocondaBot 97660a9
Add vcfdist package (#45815)
TimD1 054da76
Update r-pscbs to 0.67.0 (#45855)
BiocondaBot e3e1d1b
Update panaroo to 1.4.1 (#45863)
BiocondaBot 04ce77a
Update clipkit to 2.2.2 (#45864)
BiocondaBot e1f2b45
Update r-aroma.affymetrix to 3.2.2 (#45866)
BiocondaBot 25491a5
add snakemake-interface-report-plugins (#45871)
johanneskoester 84267ed
Update genoboo to 0.4.13 (#45620)
BiocondaBot 0196c64
Update last to 1542 (#45868)
BiocondaBot 8046679
Update pybiolib to 1.1.1749 (#45870)
BiocondaBot 512a35f
Update snakemake-interface-storage-plugins to 3.1.0 (#45874)
BiocondaBot 48a41b0
Update reframed to 1.5.1 (#45875)
BiocondaBot 35c62d9
Update snakemake-interface-common to 1.17.0 (#45876)
BiocondaBot 6ea9c6a
Update nanomotif to 0.1.19 (#45878)
BiocondaBot 93bc89f
Update harpy to 0.6.1 (#45885)
BiocondaBot 11d36ce
Add mgnify-pipelines-toolkit recipe (#45872)
chrisAta 9defd43
Update snakemake to 8.4.11 (#45882)
BiocondaBot a1a6732
Update mirmachine to 0.2.13 (#45877)
BiocondaBot 88b80b5
Update r-aroma.core to 3.3.1 (#45873)
BiocondaBot 773173c
Update tissuumaps to 3.2.0.5 (#45834)
BiocondaBot b35c3c8
Update snakemake-storage-plugin-s3 to 0.2.10 (#45835)
BiocondaBot ea8dff7
Update vcf2parquet to 0.5.0 (#45881)
BiocondaBot 9464b71
Update anglerfish to 0.6.1 (#45830)
BiocondaBot ffe575f
Update snakemake-storage-plugin-fs to 0.2.0 (#45884)
BiocondaBot c49831b
Add recipe for sctriangulate v0.13.0 (#45889)
mencian 83cd0a2
Update jbrowse2 to 2.10.2 (#45890)
BiocondaBot 0ebb57a
Update oakvar to 2.9.88 (#45891)
BiocondaBot 89f4f64
Update mgnify-pipelines-toolkit package to add missing alias for stan…
chrisAta d399eb9
Update gxf2bed to 0.2.0 (#45900)
BiocondaBot ca55f5e
Update decoupler to 1.6.0 (#45888)
BiocondaBot e6fbd9b
fix: snakemake dependencies (#45903)
johanneskoester b81545e
fix phanotate to lower than 1.6.4 (#45906)
gbouras13 ef597c9
Add initial RRIkinDP recipe (#45821)
mwaldl 8f9a056
Update nf-core to 2.13 (#45912)
BiocondaBot 711c611
Update annosine2 to 2.0.7 (#45901)
BiocondaBot ccad747
Update biocommons.seqrepo to 0.6.9 (#45898)
BiocondaBot 7097d3f
Update sevenbridges-python to 2.10.3 (#45907)
BiocondaBot 42b4594
Update pyfastani to 0.5.1 (#45908)
BiocondaBot 1ecdd4b
Update snakemake to 8.4.12 (#45911)
BiocondaBot eb1f008
Update annotsv to 3.4 (#45916)
BiocondaBot e3a6bb2
Update scanpy-scripts to 1.9.301 (#45913)
pcm32 239accc
Update mehari to 0.23.0 (#45928)
BiocondaBot 7b925f1
Update r-ontologyplot to 1.7 (#45920)
BiocondaBot b1a2708
Update metaphlan to 4.1.0 (#45926)
BiocondaBot a4ac8e1
Update snakemake-interface-common to 1.17.1 (#45930)
BiocondaBot 18bacb0
Update cramino to 0.14.3 (#45935)
BiocondaBot c8756f0
Update ngs-chew to 0.9.4 (#45934)
BiocondaBot e4c4a1a
Update trtools to 6.0.0 (#45915)
BiocondaBot 72a7572
Update pytrf to 1.3.0 (#45932)
BiocondaBot eae3ea8
Update earlgrey to 4.1.0 (#45927)
BiocondaBot 7d0612a
Update ncbi-datasets-pylib to 16.4.9 (#45918)
BiocondaBot 159bc32
Update ampcombi to 0.2.0 (#45909)
BiocondaBot a3be23f
Update bed2gff v.0.1.4 (#45923)
alejandrogzi 8d2631c
CarveMe recipe (#45799)
lhtxa 0d56752
Update bed2gtf to 1.9.1 (#45925)
BiocondaBot 66425b2
Update pcaone to 0.4.2 (#45937)
BiocondaBot 86a0823
ver 2.0.8 (#45862)
theAguy da42844
Update pronto to 2.5.6 (#45936)
BiocondaBot 68cab44
Update r-metacoder to 0.3.7 (#45904)
BiocondaBot 9ee9dfe
Update ncbi-datasets-pylib to 16.5.0 (#45938)
BiocondaBot adf37fa
Update humid to 1.0.4 (#45704)
BiocondaBot 8818735
Update trtools to 6.0.1 (#45940)
BiocondaBot d2e778d
Added ltr_harvest_parallel (#45867)
GallVp 87b39f1
Update mehari to 0.23.1 (#45947)
BiocondaBot ad5aedd
Update varlociraptor to 8.4.5 (#45950)
BiocondaBot 0f8cc80
Update ppanggolin to 2.0.3 (#45951)
BiocondaBot 73b819e
Update mehari to 0.23.2 (#45956)
BiocondaBot 5c34c19
Update dudes to 0.10.0 (#45959)
pirovc 039c73d
Update fasten to 0.8.3 (#45962)
BiocondaBot b409ac6
Update cramino to 0.14.4 (#45972)
BiocondaBot 1bc8d10
Update insilicoseq to 2.0.1 (#45971)
BiocondaBot 51bbb6e
Bump multiqc to do another build (#45969)
apeltzer 1a9c182
Update pydeseq2 to 0.4.5 (#45970)
BiocondaBot fa18703
Update panaroo to 1.4.2 (#45978)
BiocondaBot f73c561
Add IonQuant recipe. (#45126)
reid-wagner e804570
Update chewbbaca to 3.3.3 (#45975)
BiocondaBot f50482b
Update defense-finder to 1.2.2 (#45960)
BiocondaBot e59d869
Update oakvar to 2.9.89 (#45981)
BiocondaBot c5f0b4f
Update bionumpy to 1.0.4 (#45977)
BiocondaBot d819305
Add recipe epik (#45973)
blinard-BIOINFO bdb3a51
Update Woltka to 0.1.6 (#45967)
qiyunzhu 9529eb2
Update of ngs-bits to version 2024_02 (#45961)
marc-sturm ecf319b
Update hmftools-mark-dups to 1.1.1 (#45968)
BiocondaBot f05f6b8
Update pyhmmer to 0.10.6 (#45931)
BiocondaBot 33996c7
Update segmetrics to 1.4.1 (#45964)
kostrykin b802c61
Delete recipes/r-harmony directory for transfer to conda-forge (#45982)
dillonroach 6fed1aa
Update snakemake-executor-plugin-slurm to 0.3.2 (#45991)
BiocondaBot 56e0fc4
Update snakemake to 8.5.1 (#45993)
BiocondaBot 10eec08
Update snakemake to 8.5.2 (#45994)
BiocondaBot cd7a7ff
Update fiji-simple_omero_client to 5.17.0 (#45990)
BiocondaBot 98bc07f
Update isospecpy to 2.2.2 (#45986)
BiocondaBot 24ea6bf
Update augur to 24.2.3 (#45983)
BiocondaBot 01a2341
Update minute to 0.6.0 (#45976)
marcelm bb5bc0c
Update pcaone to 0.4.3 (#45974)
BiocondaBot db05f88
Update synapseclient to 4.1.0 (#45965)
BiocondaBot c109bd6
Update fgpyo to 0.1.3 (#45963)
BiocondaBot c0569ec
add libpdf support to EMBOSS (#45992)
bgruening 157efe0
Update mgnify-pipelines-toolkit to 0.1.1 (#45949)
BiocondaBot 9b06428
use circleci as artifact source (but only for packages)
daler 2e74353
Merge branch 'master' into arm-builds
daler 746450f
Merge branch 'master' into arm-builds
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# .circleci/config.yml | ||
version: 2.1 | ||
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||
executors: | ||
osx-arm64: | ||
macos: | ||
xcode: 14.2.0 # indicate your selected version of Xcode | ||
resource_class: macos.m1.large.gen1 | ||
linux-aarch64: | ||
machine: | ||
image: ubuntu-2004:current | ||
resource_class: arm.medium | ||
|
||
jobs: # a basic unit of work in a run | ||
build_and_test: | ||
parameters: | ||
os: | ||
type: executor | ||
executor: << parameters.os >> | ||
steps: | ||
- checkout | ||
|
||
- run: | ||
name: Fetch bioconda install script | ||
command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/install-and-set-up-conda.sh | ||
|
||
- restore_cache: | ||
keys: | ||
- bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} | ||
|
||
- run: | ||
name: Install bioconda-utils | ||
command: | | ||
sudo mkdir -p /opt/miniconda | ||
sudo chown -R $USER /opt/miniconda | ||
bash install-and-set-up-conda.sh | ||
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||
|
||
- save_cache: | ||
key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} | ||
paths: | ||
- /opt/miniconda | ||
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||
|
||
- run: | ||
name: Build and test | ||
command: | | ||
conda activate bioconda-utils | ||
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bioconda-utils build recipes config.yml --git-range origin/master HEAD | ||
|
||
- run: | ||
name: Prepare artifacts | ||
command: | | ||
( | ||
mkdir -p /tmp/artifacts/packages | ||
cd /opt/miniconda/envs/bioconda/conda-bld || exit 0 | ||
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find -name .cache | xargs rm -rf || true | ||
for n in index.html channeldata.json linux-64 osx-64 noarch; do | ||
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cp -rv $n /tmp/artifacts/packages || true | ||
done | ||
) || true | ||
|
||
- store_artifacts: | ||
path: /tmp/artifacts | ||
|
||
build_and_push: | ||
parameters: | ||
os: | ||
type: executor | ||
executor: << parameters.os >> | ||
steps: | ||
- checkout | ||
|
||
- run: | ||
name: Fetch bioconda install script | ||
command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/install-and-set-up-conda.sh | ||
|
||
- restore_cache: | ||
keys: | ||
- bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} | ||
|
||
- run: | ||
name: Install bioconda-utils | ||
command: | | ||
sudo mkdir -p /opt/miniconda | ||
chown -R $USER:$USER /opt/miniconda | ||
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||
bash install-and-set-up-conda.sh | ||
|
||
- save_cache: | ||
key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} | ||
paths: | ||
- /opt/miniconda | ||
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- run: | ||
name: Build and push | ||
command: | | ||
conda activate bioconda-utils | ||
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# TODO we need to update bioconda-utils with support for retrieving circleci artifacts from above | ||
bioconda-utils handle-merged-pr recipes config.yml \ | ||
--repo bioconda/bioconda-recipes \ | ||
--git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ | ||
--fallback build | ||
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workflows: | ||
build_and_test: | ||
jobs: | ||
- build_and_test: | ||
filters: | ||
branches: | ||
ignore: master | ||
matrix: | ||
parameters: | ||
os: [osx-arm64, linux-aarch64] | ||
build_and_push: | ||
jobs: | ||
- build_and_push: | ||
filters: | ||
branches: | ||
only: master | ||
matrix: | ||
parameters: | ||
os: [osx-arm64, linux-aarch64] |
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It might be useful:
Since recently it is possible to use Docker executor with ARM64 resources - https://circleci.com/docs/using-docker/#arm
This way you could use a custom Docker image that has most of the dependencies preinstalled. It will save a lot of time for the runs/builds!
Here is a small example:
Here I use
openEuler
Linux. CircleCI provides only Ubuntu images for themachine
executor. You could use CentOS (or even better - RockyLinux) as the other base images.