gatingset_to_flowjo gate not found; version problem? #126
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Can you share the minimum reproducible example? |
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Can you try the file I sent you around the 18th? |
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I think I know where the problem is. Let me tackle this and get back to you once we have a solution. |
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I've pushed the fix. You will need to pull the latest CytoML from github master and pull the new docker image |
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I have pulled the image but cannot run it: I am not a docker expert and don't know what to do with status 132 or "Resource temporarily unavailable" |
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Originally I ran into this problem: I am not sure why the temp file doesn't exist as well. Thx for looking into this. |
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I don't know how to reproduce your error, here is what you should get when you run the command at termainal |
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Hi Mike, But, again, this doesn't mean much to me. Before upgrading the OS, which I really like to push to some time with less stress, I would like to ask you for the script to create the docker file. Maybe I can get this working. Thanks for you consideration. |
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docker is os and machine independent , shouldn't behave differently. Here is a reproducible example see if it works for you |
Unfortunately, there are some specific issues with MAC as it is running a different VM. These sites are not 100% matching, but they show some aspects of the issue. I can access the executable within the docker file, but it would be helpful to see the docker file to create the image such that I can verify the machine and then the executable. I guess there are certain libraries that are responsible for the interaction between the VM, mac OS and Linux which are not behaving. Btw. I was able to verify that the mounting of files works, i.e. I can access the the files from my Mac from within the docker image. (at /gs) |
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here is the dockerfile I am not sure how much help you can get from it, since the |
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here is the dockerfile I am not sure how much help you can get from it, since the |
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Sorry, still not working. As a last resort, I even updated the OS to Big Sur. I installed gdb within the VM and traced back the illegal instruction to:
for the shlx command I found out that it might be that my computer is too old (2013, Ivy Bridge EP, Xeon E5) is not supporting AVX2. (I also tried copying the executable into a new VM, without luck.) Would it be possible to compile it on my side within the VM or even directly on MacOS? |
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Does it mean that docker in general isn't working in your mac vm? Can you enter bash mode by |
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docker is working. I can run R within Docker. Version 2.0 is running normally: Other docker images are running as well. |
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Mike, the docker image produces the correct output: |
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Do you have any idea what could be the cause of the problem? |
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Hi Mike, not sure if you understood, that the VM is working and I found a more recent computer that runs the program. thanks, Bernd |
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I've updated the docker image, with latest pull, your previous error should be gone. But this time, you should see which tells you that your gs has the logical gate from |
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Just as a side-note: yesterday I received a new computer, a MacBook pro. The chip is now called: "Apple M1" There is only a RC (version 2) with quite a few unresolved issues. This whole thing is turning into a nightmare. I will try with a windows based computer from my son |
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I hope we can get closer with this. It is not a "minimal" example but has all the elements I am using. with the following error message: |
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First of all, if you pull the latest docker image , you should see Secondly, you were creating the I think what you may want to do is to add these bool vector as a single factor , which will be treated the clustering results. And it can be handled by flowjo properly |
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I am getting the following error on M1 Pro chip Macbook Pro. I installed docker, got the latest dev version of flowCore, CytoML. But I am getting this weird msg on specifying image platform, for which i dont see any options to specify it. Please advise.
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I was able to fix the issue by adding ❯ docker inspect -f '{{.Os}}/{{.Architecture}}' public.ecr.aws/ozette/cytoverse/gs-to-wsp
linux/amd64
❯ docker info -f '{{.OSType}}/{{.Architecture}}'
linux/aarch64 As a temporary fix, copy and source the following gatingset_to_flowjo <- function (gs, outFile, showHidden = FALSE, docker_img = NULL, ...) {
res <- CytoML:::check_binary_status()
if (res != "binary_ok") {
res <- CytoML:::check_docker_status(docker_img)
}
if (!(res[1] %in% c("binary_ok", "docker_ok")))
stop(res)
if (is(gs, "GatingSet")) {
tmp <- tempfile()
suppressMessages(save_gs(gs, tmp, ...))
}
else tmp <- gs
outFile <- gsub(" ", "\\\\ ", file.path(normalizePath(dirname(outFile)),
basename(outFile)))
tmpfile <- tempfile()
if (res[1] == "binary_ok") {
message("Using local gs-to-flowjo binary to write FlowJo workspace...")
res <- suppressWarnings(system2("gs-to-flowjo", paste0(" --src=",
tmp, " --dest=", tmpfile, " --showHidden=", showHidden),
stderr = TRUE))
}
else {
docker_img <- res[2]
v1 <- packageVersion("cytolib")
v2 <- system2("docker", paste0("run --platform linux/amd64", docker_img, " --cytolib-version"),
stdout = TRUE)
message(paste0("Using docker image ", docker_img, " to write FlowJo workspace..."))
res <- suppressWarnings(system2("docker", paste0("run --platform linux/amd64",
" -v ", tmp, ":/gs", " -v ", normalizePath(dirname(tmpfile)),
":/out ", docker_img, " --src=/gs --dest=/out/",
basename(tmpfile), " --showHidden=", showHidden),
stderr = TRUE))
}
if (length(res) > 0)
stop(res)
else {
tree <- xml2::read_xml(tmpfile)
CytoML:::add_version_info(tree)
invisible(xml2::write_xml(tree, file = outFile))
}
}This will allow Docker to use emulation. If it still fails, make sure to install Rosetta 2. Long term, I think it should be rebuilt for multiple-architectures. @mikejiang |
I want to export a gatingset to FlowJo. (the data origniates from a flowJo workspace, is a bit modified (added a gate and two markers)
I get the error message below, complaining about a population ("Treg_Memory-") that is not found.
I cannot find this population myself either:
I am also wondering if this has to do with the warning about 2.3.0 vs. 2.3.7.
Not sure what to test next. Any help appreciated.
Thanks,
Bernd
PS. not sure if these are related, but with the same data set, only a bit more modified, I get the following error message:
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