Dear Dynmethods team,
I'm working with single cell data and as part of our data analysis we would like to perform trajectory inference. Since dynverse offers a wide range of TI methods, I was very excited to try this. However, I've run into some trouble with the infer_trajectory() function. When docker is running it appears to download the correct image and afterwards attempts to run it. At this point lies my problem as the function appears to run a few seconds after which I get a prompt, but no output. Since I'm working with an Apple Silicon based MacBook Pro, I thought the architecture of the chip was causing the issue. However, when I tried the same code on an Intel based MacBook Pro, I had the same issue.
I've run test_docker_installation on both Macs and this is the output:
✔ Docker is installed
✔ Docker daemon is running
✔ Docker is at correct version (>1.0): 1.41
✔ Docker is in linux mode
✔ Docker can pull images
✔ Docker can run image
✔ Docker can mount temporary volumes
✔ Docker test successful -----------------------------------------------------------------
[1] TRUE
My docker installation thus appears to be fine. I then thought my data might be the problem and thus downloaded the example data provided by dynverse. However, infer_trajectory() failed here as well. Am I doing something wrong? What can I do to fix this?
Kind regards,
Laurenz De Cock
Code for example dataset:
Dynverse Example Dataset
Load Required Libraries
library(Seurat)
library(ggplot2)
library(dynmethods)
library(dynwrap)
library(Matrix)
library(tidyr)
Load Example Dataset
example_dataset <- dynwrap::example_dataset
Prepare Data
dataset <- wrap_expression(
expression = example_dataset$expression,
counts = example_dataset$counts
)
dataset <- add_prior_information(
dataset,
start_id = "Cell1"
)
dataset <- add_dimred(
dataset,
example_dataset$dimred
)
Run trajectory inference
model <- infer_trajectory(dataset, ti_comp1())
Dear Dynmethods team,
I'm working with single cell data and as part of our data analysis we would like to perform trajectory inference. Since dynverse offers a wide range of TI methods, I was very excited to try this. However, I've run into some trouble with the infer_trajectory() function. When docker is running it appears to download the correct image and afterwards attempts to run it. At this point lies my problem as the function appears to run a few seconds after which I get a prompt, but no output. Since I'm working with an Apple Silicon based MacBook Pro, I thought the architecture of the chip was causing the issue. However, when I tried the same code on an Intel based MacBook Pro, I had the same issue.
I've run test_docker_installation on both Macs and this is the output:
✔ Docker is installed
✔ Docker daemon is running
✔ Docker is at correct version (>1.0): 1.41
✔ Docker is in linux mode
✔ Docker can pull images
✔ Docker can run image
✔ Docker can mount temporary volumes
✔ Docker test successful -----------------------------------------------------------------
[1] TRUE
My docker installation thus appears to be fine. I then thought my data might be the problem and thus downloaded the example data provided by dynverse. However, infer_trajectory() failed here as well. Am I doing something wrong? What can I do to fix this?
Kind regards,
Laurenz De Cock
Code for example dataset:
Dynverse Example Dataset
Load Required Libraries
library(Seurat)
library(ggplot2)
library(dynmethods)
library(dynwrap)
library(Matrix)
library(tidyr)
Load Example Dataset
example_dataset <- dynwrap::example_dataset
Prepare Data
dataset <- wrap_expression(
expression = example_dataset$expression,
counts = example_dataset$counts
)
dataset <- add_prior_information(
dataset,
start_id = "Cell1"
)
dataset <- add_dimred(
dataset,
example_dataset$dimred
)
Run trajectory inference
model <- infer_trajectory(dataset, ti_comp1())