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Jake VanCampen jakevc Providence Portland, OR Bioinformatics Scientist

jakevc/karyopype 1

A chromosomal visualization package for python.

jakevc/ATACseqQC 0

ATAC-seq Quality Control

jakevc/aws_pipeline_test 0

Test snakemake pipeline on aws ec2

jakevc/bedCons 0

Calculate conservation statistics over regions in a BED file, from a phyloP or phastCons bigWig

jakevc/bioconda-recipes 0

Conda recipes for the bioconda channel.

jakevc/bio_610B 0

Course materials for Advanced Biological Statistics II, Bio 610B, at the University of Oregon.

jakevc/cocoa-eh-hugo-theme 0

A enhanced version of Cocoa. Clean, fast, and responsive theme with cool typography.

jakevc/conda-package-publish-action 0

Github Action to deploy conda package to Anaconda repository

pull request commentsnakemake/snakemake

WIP: Azure Batch integration

Would love to see this pulled in @andreas-wilm @johanneskoester.

andreas-wilm

comment created time in a month

issue commentliulab-dfci/TRUST4

Fails with uninformative error

Hi, I think you are right. I did recompile with -O, then switched to a machine with more memory and the run finished. After observing the memory usage during runtime, it appears that was the issue. Anyhow, if there was some way to return an informative error when the program runs out of memory that would be useful for future users. Thanks!

jakevc

comment created time in 2 months

startedOTA-Insight/bqwriter

started time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

Just kidding that eventually failed also with:

system /trust4-clean/trust4  -f refs/hg38_bcrtcr.fa --trimLevel 2 --skipMateExtension -t 16 -o ./foxlab-trust4/run1 -u ./foxlab-trust4/run1_toassemble.fq --barcode ./foxlab-trust4/run1_toassemble_bc.fa --UMI ./foxlab-trust4/run1_toassemble_umi.fa failed: 9 at trust4-clean/run-trust4 line 48.
jakevc

comment created time in 2 months

issue commentterraform-google-modules/terraform-google-container-vm

Restart policy kills konlet-startup container

But here they are not: https://github.com/GoogleCloudPlatform/konlet/blob/9cb9106daf07123c2641159cb8bcc9d6f4960ec2/gce-containers-startup/types/api.go#L21

jakevc

comment created time in 2 months

issue commentterraform-google-modules/terraform-google-container-vm

Restart policy kills konlet-startup container

Here is some restart policy logic in the konlet service that contains "no"...

https://github.com/GoogleCloudPlatform/konlet/blob/9cb9106daf07123c2641159cb8bcc9d6f4960ec2/gce-containers-startup/runtime/runtime.go#L283

jakevc

comment created time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

Ahh there we are, okay so without --barcodeWhiteList we are cookin with heat.

trust4-clean/run-trust4 -t 8 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/*_R2_*.fastq.gz --barcode data/*_R1_*.fastq.gz --barcodeRange 0 15 + --UMI data/*_R1_*.fastq.gz --umiRange 16 25 + --repseq

That command works

jakevc

comment created time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

$ cat /etc/os-release
NAME="Ubuntu"
VERSION="21.04 (Hirsute Hippo)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 21.04"
VERSION_ID="21.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=hirsute
UBUNTU_CODENAME=hirsute
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 10.3.0-1ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-gDeRY6/gcc-10-10.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-gDeRY6/gcc-10-10.3.0/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 10.3.0 (Ubuntu 10.3.0-1ubuntu1)
jakevc

comment created time in 2 months

issue commentterraform-google-modules/terraform-google-container-vm

Restart policy kills konlet-startup container

It's worth noting that even when supplying the values "never" or "on-failure", when I look at the vm metadata it still shows up as "Always".

jakevc

comment created time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

It's also worth noting that I got a segfault with the conda install, but I can file that as a separate issue

jakevc

comment created time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

same same

$ trust4-clean/run-trust4 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --barcodeRange 0 15 + --UMI data/B-A1_S6_L001_R1_001.fastq.gz --umiRange 16 25 + --repseq --barcodeWhitelist refs/737K-august-2016.txt
[Thu Nov 18 18:25:46 2021] TRUST4 begins.
[Thu Nov 18 18:25:46 2021] SYSTEM CALL: /home/jake.vancampenprovidence.org/yoshi-trust4/trust4-clean/fastq-extractor -t 1 -f refs/hg38_bcrtcr.fa -o ./foxlab-trust4/run1_toassemble  --barcodeStart 0 --barcodeEnd 15 --umiStart 16 --umiEnd 25 --barcodeWhitelist refs/737K-august-2016.txt -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --UMI data/B-A1_S6_L001_R1_001.fastq.gz
[Thu Nov 18 18:25:46 2021] Start to extract candidate reads from read files.
Unknown parameter (null)
system /home/jake.vancampenprovidence.org/yoshi-trust4/trust4-clean/fastq-extractor -t 1 -f refs/hg38_bcrtcr.fa -o ./foxlab-trust4/run1_toassemble  --barcodeStart 0 --barcodeEnd 15 --umiStart 16 --umiEnd 25 --barcodeWhitelist refs/737K-august-2016.txt -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --UMI data/B-A1_S6_L001_R1_001.fastq.gz failed: 256 at trust4-clean/run-trust4 line 48.
jakevc

comment created time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

Yup that works

$ trust4-clean/run-trust4 -t 8 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/B-A1_S6_L001_R2_001.fastq.gz --repseq
[Thu Nov 18 18:18:42 2021] TRUST4 begins.
[Thu Nov 18 18:18:42 2021] SYSTEM CALL: /yoshi-trust4/trust4-clean/fastq-extractor -t 8 -f refs/hg38_bcrtcr.fa -o ./foxlab-trust4/run1_toassemble  -u data/B-A1_S6_L001_R2_001.fastq.gz
[Thu Nov 18 18:18:42 2021] Start to extract candidate reads from read files.
[Thu Nov 18 18:19:27 2021] Finish extracting reads.
[Thu Nov 18 18:19:27 2021] SYSTEM CALL: /yoshi-trust4/trust4-clean/trust4  -t 8 -f refs/hg38_bcrtcr.fa --trimLevel 2 --skipMateExtension -o ./foxlab-trust4/run1 -u ./foxlab-trust4/run1_toassemble.fq
[Thu Nov 18 18:19:27 2021] Found 2346 reads.
[Thu Nov 18 18:19:27 2021] Finish sorting the reads.
[Thu Nov 18 18:19:27 2021] Finish rough annotations.
[Thu Nov 18 18:19:27 2021] Assembled 41 reads.
[Thu Nov 18 18:19:27 2021] Try to rescue 17 reads for assembly.
[Thu Nov 18 18:19:27 2021] Rescued 0 reads.
[Thu Nov 18 18:19:27 2021] SYSTEM CALL: /yoshi-trust4/trust4-clean/annotator -f refs/human_IMGT+C.fa -a ./foxlab-trust4/run1_final.out -t 8 -o ./foxlab-trust4/run1  -r ./foxlab-trust4/run1_assembled_reads.fa > ./foxlab-trust4/run1_annot.fa
[Thu Nov 18 18:19:27 2021] Start to annotate assemblies.
[Thu Nov 18 18:19:27 2021] Start to realign reads for CDR3 analysis.
[Thu Nov 18 18:19:27 2021] Compute CDR3 abundance.
[Thu Nov 18 18:19:27 2021] Finish annotation.
[Thu Nov 18 18:19:27 2021] SYSTEM CALL: perl /yoshi-trust4/trust4-clean/trust-simplerep.pl ./foxlab-trust4/run1_cdr3.out  > ./foxlab-trust4/run1_report.tsv
[Thu Nov 18 18:19:27 2021] SYSTEM CALL: perl /yoshi-trust4/trust4-clean/trust-airr.pl ./foxlab-trust4/run1_cdr3.out ./foxlab-trust4/run1_annot.fa > ./foxlab-trust4/run1_airr.tsv
[Thu Nov 18 18:19:28 2021] TRUST4 finishes.
jakevc

comment created time in 2 months

issue commentliulab-dfci/TRUST4

Fails with uninformative error

Interesting, yeah appears to be the same error with just one

$ ./TRUST4/run-trust4 --od ./foxlab-trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --barcodeRange 0 15 + --UMI data/B-A1_S6_L001_R1_001.fastq.gz --umiRange 16 25 + --repseq --barcodeWhitelist refs/737K-august-2016.txt
[Thu Nov 18 05:01:50 2021] TRUST4 begins.
[Thu Nov 18 05:01:50 2021] SYSTEM CALL: /home/jake.vancampenprovidence.org/yoshi-trust4/TRUST4/fastq-extractor -t 1 -f refs/hg38_bcrtcr.fa -o ./foxlab-trust4/run1_toassemble  --barcodeStart 0 --barcodeEnd 15 --umiStart 16 --umiEnd 25 --barcodeWhitelist refs/737K-august-2016.txt -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --UMI data/B-A1_S6_L001_R1_001.fastq.gz
[Thu Nov 18 05:01:50 2021] Start to extract candidate reads from read files.
Unknown parameter (null)
system /home/jake.vancampenprovidence.org/yoshi-trust4/TRUST4/fastq-extractor -t 1 -f refs/hg38_bcrtcr.fa -o ./foxlab-trust4/run1_toassemble  --barcodeStart 0 --barcodeEnd 15 --umiStart 16 --umiEnd 25 --barcodeWhitelist refs/737K-august-2016.txt -u data/B-A1_S6_L001_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --UMI data/B-A1_S6_L001_R1_001.fastq.gz failed: 256 at ./TRUST4/run-trust4 line 48.
jakevc

comment created time in 2 months

issue openedliulab-dfci/TRUST4

Fails with uninformative error

When running with the command:

./TRUST4/run-trust4 --od ./trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/*_R2_*.fastq.gz --barcode data/*_R1_*.fastq.gz --barcodeRange 0 15 + --UMI data/*_R1_*.fastq.gz --umiRange 16 25 + --repseq --barcodeWhitelist refs/737K-august-2016.txt

Fails with output:

[Wed Nov 17 23:39:31 2021] TRUST4 begins.
[Wed Nov 17 23:39:31 2021] SYSTEM CALL: TRUST4/fastq-extractor -t 1 -f refs/hg38_bcrtcr.fa -o ./run1_toassemble  --barcodeStart 0 --barcodeEnd 15 --umiStart 16 --umiEnd 25 --barcodeWhitelist refs/737K-august-2016.txt -u data/B-A1_S6_L001_R2_001.fastq.gz -u data/B-A1_S6_L002_R2_001.fastq.gz -u data/B-B1_S4_L001_R2_001.fastq.gz -u data/B-B1_S4_L002_R2_001.fastq.gz -u data/B-M1_S2_L001_R2_001.fastq.gz -u data/B-M1_S2_L002_R2_001.fastq.gz -u data/T-A1_S5_L001_R2_001.fastq.gz -u data/T-A1_S5_L002_R2_001.fastq.gz -u data/T-M1_S1_L001_R2_001.fastq.gz -u data/T-M1_S1_L002_R2_001.fastq.gz -u data/T-T1_S3_L001_R2_001.fastq.gz -u data/T-T1_S3_L002_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --barcode data/B-A1_S6_L002_R1_001.fastq.gz --barcode data/B-B1_S4_L001_R1_001.fastq.gz --barcode data/B-B1_S4_L002_R1_001.fastq.gz --barcode data/B-M1_S2_L001_R1_001.fastq.gz --barcode data/B-M1_S2_L002_R1_001.fastq.gz --barcode data/T-A1_S5_L001_R1_001.fastq.gz --barcode data/T-A1_S5_L002_R1_001.fastq.gz --barcode data/T-M1_S1_L001_R1_001.fastq.gz --barcode data/T-M1_S1_L002_R1_001.fastq.gz --barcode data/T-T1_S3_L001_R1_001.fastq.gz --barcode data/T-T1_S3_L002_R1_001.fastq.gz --UMI data/B-A1_S6_L001_R1_001.fastq.gz --UMI data/B-A1_S6_L002_R1_001.fastq.gz --UMI data/B-B1_S4_L001_R1_001.fastq.gz --UMI data/B-B1_S4_L002_R1_001.fastq.gz --UMI data/B-M1_S2_L001_R1_001.fastq.gz --UMI data/B-M1_S2_L002_R1_001.fastq.gz --UMI data/T-A1_S5_L001_R1_001.fastq.gz --UMI data/T-A1_S5_L002_R1_001.fastq.gz --UMI data/T-M1_S1_L001_R1_001.fastq.gz --UMI data/T-M1_S1_L002_R1_001.fastq.gz --UMI data/T-T1_S3_L001_R1_001.fastq.gz --UMI data/T-T1_S3_L002_R1_001.fastq.gz
[Wed Nov 17 23:39:31 2021] Start to extract candidate reads from read files.
Unknown parameter (null)
system TRUST4/fastq-extractor -t 1 -f refs/hg38_bcrtcr.fa -o ./run1_toassemble  --barcodeStart 0 --barcodeEnd 15 --umiStart 16 --umiEnd 25 --barcodeWhitelist refs/737K-august-2016.txt -u data/B-A1_S6_L001_R2_001.fastq.gz -u data/B-A1_S6_L002_R2_001.fastq.gz -u data/B-B1_S4_L001_R2_001.fastq.gz -u data/B-B1_S4_L002_R2_001.fastq.gz -u data/B-M1_S2_L001_R2_001.fastq.gz -u data/B-M1_S2_L002_R2_001.fastq.gz -u data/T-A1_S5_L001_R2_001.fastq.gz -u data/T-A1_S5_L002_R2_001.fastq.gz -u data/T-M1_S1_L001_R2_001.fastq.gz -u data/T-M1_S1_L002_R2_001.fastq.gz -u data/T-T1_S3_L001_R2_001.fastq.gz -u data/T-T1_S3_L002_R2_001.fastq.gz --barcode data/B-A1_S6_L001_R1_001.fastq.gz --barcode data/B-A1_S6_L002_R1_001.fastq.gz --barcode data/B-B1_S4_L001_R1_001.fastq.gz --barcode data/B-B1_S4_L002_R1_001.fastq.gz --barcode data/B-M1_S2_L001_R1_001.fastq.gz --barcode data/B-M1_S2_L002_R1_001.fastq.gz --barcode data/T-A1_S5_L001_R1_001.fastq.gz --barcode data/T-A1_S5_L002_R1_001.fastq.gz --barcode data/T-M1_S1_L001_R1_001.fastq.gz --barcode data/T-M1_S1_L002_R1_001.fastq.gz --barcode data/T-T1_S3_L001_R1_001.fastq.gz --barcode data/T-T1_S3_L002_R1_001.fastq.gz --UMI data/B-A1_S6_L001_R1_001.fastq.gz --UMI data/B-A1_S6_L002_R1_001.fastq.gz --UMI data/B-B1_S4_L001_R1_001.fastq.gz --UMI data/B-B1_S4_L002_R1_001.fastq.gz --UMI data/B-M1_S2_L001_R1_001.fastq.gz --UMI data/B-M1_S2_L002_R1_001.fastq.gz --UMI data/T-A1_S5_L001_R1_001.fastq.gz --UMI data/T-A1_S5_L002_R1_001.fastq.gz --UMI data/T-M1_S1_L001_R1_001.fastq.gz --UMI data/T-M1_S1_L002_R1_001.fastq.gz --UMI data/T-T1_S3_L001_R1_001.fastq.gz --UMI data/T-T1_S3_L002_R1_001.fastq.gz failed: 256 at ./TRUST4/run-trust4 line 48.

I complied from source, i.e. git pull & make.

created time in 2 months

issue openedterraform-google-modules/terraform-google-container-vm

Restart policy kills konlet-startup container

TL;DR

When supplying the restart policy "No" in the terraform configuration, the konlet-startup container fails.

Expected behavior

I expect the konlet-startup container to run correctly.

Observed behavior

The konlet startup container fails with:

Nov 17 18:49:15 gcs-inventory konlet-startup[3383]: 2021/11/17 18:49:15 Error: Failed to start container: Invalid container declaration: Unsupported container restart policy 'No'

Terraform Configuration

# cloud runner service for cloud storage inventory
terraform {
  required_providers {
    google = {
      source  = "hashicorp/google"
      version = "~> 3.80"
    }
  }
}

provider "google" {
  project = var.project.name
  zone    = var.project.zone
}

resource "google_compute_firewall" "http-traffic" {
  name    = "allow-http"
  network = "default"

  allow {
    protocol = "tcp"
    ports    = ["80"]
  }

  target_tags = ["http-traffic"]
}

resource "google_compute_firewall" "http-ssh" {
  name    = "allow-ssh"
  network = "default"

  allow {
    protocol = "tcp"
    ports    = ["22"]
  }

  target_tags = ["ssh-traffic"]
}

data "terraform_remote_state" "setup" {
  backend = "local"

  config = {
    path = "setup/terraform.tfstate"
  }
}

module "gce-container" {
  source = "github.com/terraform-google-modules/terraform-google-container-vm"

  cos_image_name = var.instance.image

  container = {
    image = data.terraform_remote_state.setup.outputs.image

    env = [
      {
        name  = "BUCKET"
        value = var.bucket
      },
      {
        name  = "GCLOUD_PROJECT"
        value = var.project.name
      },
      {
        name  = "BQ_DATASET"
        value = var.bqdataset
      },
      {
        name  = "BQ_TABLE"
        value = var.bqtable
      }
    ]

    volumeMounts = [
      {
        mountPath = "/cache"
        name      = "tempfs-0"
        readOnly  = false
      },
    ]
  }

  volumes = [
    {
      name = "tempfs-0"

      emptyDir = {
        medium = "Memory"
      }
    },
  ]

  restart_policy = "no"
}

# single vm
resource "google_compute_instance" "cos-vm" {
  name         = var.service_name
  machine_type = var.instance.type
  project      = var.project.name
  zone         = var.project.zone
  tags         = ["ssh-traffic", "http-traffic"]

  boot_disk {
    initialize_params {
      image = module.gce-container.source_image
      size  = var.instance.image_size
      type  = var.instance.image_type
    }
  }

  network_interface {
    network = "default"
    access_config {}
  }

  metadata = {
    gce-container-declaration = module.gce-container.metadata_value
    google-logging-enabled    = "true"
    google-monitoring-enabled = "true"
  }

  labels = {
    container-vm = module.gce-container.vm_container_label
  }

  service_account {
    email  = data.terraform_remote_state.setup.outputs.serivce_account_email
    scopes = ["cloud-platform"]
  }
}

Terraform Version

terraform version
Terraform v1.0.2
on darwin_amd64
+ provider registry.terraform.io/hashicorp/google v3.90.1
+ provider registry.terraform.io/hashicorp/google-beta v4.1.0
+ provider registry.terraform.io/hashicorp/template v2.2.0

Additional information

My container does run when using the restart policies supported in the documentation, "never", "on-failure", or "always", but I have not been able to verify that their behavior is as expected.

created time in 2 months

CommitCommentEvent
CommitCommentEvent

startedwelch-lab/liger

started time in 2 months

issue commentSage-Bionetworks/Genie

Keyring version not compatible with python 3.10

Interestingly, SynapsePythonClient is stable using the older keyring and python3.10...

jakevc

comment created time in 2 months

issue openedSage-Bionetworks/Genie

Update keyring version requirement for python3.10

Insatlled genie in new conda environment with python3.10

conda create -n genie python
conda activate genie
pip install aacrgenie

The tool panics with the following error from the keyring backend:

ImportError: cannot import name 'Callable' from 'collections' 

Turns out whatever version of keyring is not compatible with python3.10:

python -c "import keyring as package; print(package.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/jake.vancampenprovidence.org/miniconda3/envs/genie/lib/python3.10/site-packages/keyring/__init__.py", line 3, in <module>
    from .core import (set_keyring, get_keyring, set_password, get_password,
  File "/Users/jake.vancampenprovidence.org/miniconda3/envs/genie/lib/python3.10/site-packages/keyring/core.py", line 13, in <module>
    from . import backend
  File "/Users/jake.vancampenprovidence.org/miniconda3/envs/genie/lib/python3.10/site-packages/keyring/backend.py", line 13, in <module>
    from .util import properties
  File "/Users/jake.vancampenprovidence.org/miniconda3/envs/genie/lib/python3.10/site-packages/keyring/util/properties.py", line 1, in <module>
    from collections import Callable
ImportError: cannot import name 'Callable' from 'collections' (/Users/jake.vancampenprovidence.org/miniconda3/envs/genie/lib/python3.10/collections/__init__.py)

Upgraded to keyring latest and solved the problem:

pip install -I keyring==23.2.1
genie -v
genie 12.5.0

This is due to a change in the python standard library: https://docs.python.org/3/library/collections.abc.html, so could also be solved by downgrading to a different python version.

created time in 2 months

starteddomZippilli/gcs-proxy-cloud-run

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issue commentsnakemake/snakemake

Usage Q - Run all rules for a given wildcard before going through to the next "batch"

You can indirectly tune that behavior using --jobs [N], assuming each sample can be executed all the way through the DAG independently.

aleighbrown

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