function

[ryao-mdanderson]

Dear crisprVerse support team,

I am an HPC system admin and helping researcher in our institution to use CriprVerse docker container.

Reading site https://github.com/crisprVerse/Docker says:

"We offer Docker images of the crisprVerse ecosystem on the Docker Hub. The image contains the following components:

R installation (currently 4.2.1)
crisprVerse R packages and their dependencies
ViennaRNA 2.5.1
RNAhybrid 2.1.2
Conveniently, all Python conda environments needed for crisprScore are also already installed in the Docker image."

The last line indicated the conda environments are needed for criprScore. I appreciate this.

Test the container, seems the function addOnTargetScores() works for a limited algorithms? Here are the tests step inside the container:

$ apptainer run /risapps/apptainer/repo/crisprverse/20240702/crisprverse_dev.sif /bin/bash
$ R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"

.libPaths("/home/crisprverse/usr/local/lib/R/site-library") ---> changed it to use the R path inside the container
library(crisprScore)
library(crisprDesign)
library(BSgenome.Hsapiens.UCSC.hg38)
library(basilisk)

basilisk.utils::getExternalDir()
[1] "/home/xxx/.cache/R/basilisk/1.9.3"
data(SpCas9, package="crisprBase")
gr <- queryTxObject(
txObject=grListExample,
featureType="cds",
queryColumn="gene_symbol",
queryValue="IQSEC3")
guideSet <- findSpacers(
gr,
bsgenome=BSgenome.Hsapiens.UCSC.hg38,
crisprNuclease=SpCas9)
addOnTargetScores(guideSet)
addOnTargetScores] Adding azimuth scores.

[addOnTargetScores] Adding deephf scores.

|======================================================================| 100%

snapshotDate(): 2022-04-26
see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation
loading from cache
Error in checkForRemoteErrors(lapply(cl, recvResult)) :
one node produced an error: could not find function "activateEnvironment"

However, if put an method "azimuth",
when I run gs2 <- addOnTargetScores(guideSet, method = "azimuth"). it works.

But adding a method "deephf", gs2 <- addOnTargetScores(guideSet, method = "deephf"). hit an error message:
"... could not find function "activateEnvironment..."

Seems there are list of methods available for the function; Please advise if I missed anything to have "deephf" working?
methods = c("azimuth", "ruleset1", "ruleset3", "lindel", "deepcpf1", "deephf",
"deepspcas9", "enpamgb", "casrxrf", "crisprater", "crisprscan")

Thank you for your help,
Rong Yao

[ryao-mdanderson]

Dear crisprVerse support team, @Jfortin1 @developerpiru @ltHobbes

May you please help me with the above question? I appreciate any suggestions with using the container.

Thanks,
Rong

[Jfortin1]

Hi Rong @ryao-mdanderson ,

We'll work on a new Docker image in the next few weeks after fixing a few of the python environments needed for the scoring algorithm. We'll keep you in the loop.

[ryao-mdanderson]

Hello Jean-Philippe @Jfortin1,

Awesome! Look forward to the new docker image:)

Best,
Rong

[ryao-mdanderson]

Hello @Jfortin1,

Just a follow up, do you have any chance to work on the new docker image?

Thank you!
Rong