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How to install docker4seq in windows OS #1

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kagningemma opened this issue Jul 12, 2017 · 12 comments
Open

How to install docker4seq in windows OS #1

kagningemma opened this issue Jul 12, 2017 · 12 comments

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@kagningemma
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Thank you very much for providing this docker4seq package for R. I am a trying to learn NGS data analysis using docker4seq package but I am facing problems downloading the docker4seq package using Rstudio on windows 7 OS ( Intel Xeon CPU E5-1603 @2.8GHz, HD 1 TB, RAM 32GB). I have docker for windows installed as well as the 7 containers listed at the "02 requirements" section here http://rpubs.com/rcaloger/280163.

I pulled+ran the images of the 7 containers, and ran the "install_github("kendomaniac/docker4seq") command in Rstudio, but it didn`t work. instead, i got the following error message in R:

library(devtools)
Warning message:
Package 'devtools' was built under R version 3.4.1

install_github("kendomaniac/docker4seq")
Downloading GitHub repo kendomaniac/docker4seq@master
from URL https://api.github.com/repos/kendomaniac/docker4seq/zipball/master
Installing docker4seq
"C:/PROGRA1/R/R-341.0/bin/x64/R" --no-site-file --no-environ --no-save
--no-restore --quiet CMD INSTALL
"C:/Users/viro10/AppData/Local/Temp/RtmpOGpjw0/devtools7bc7ee232e6/kendomaniac-docker4seq-3643254"
--library="C:/Program Files/R/R-3.4.0/library" --install-tests

  • installing source package 'docker4seq' ...
    ** R
    Warning: 'casc.scnorm.R' (2 lines) can not be re-encoded
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    *** arch - i386
    Error: package or namespace load failed for 'docker4seq' in namespaceExport(ns, exports):
    undefined exports: cascStep4
    Error: Loading failed
      Execution stopped
    *** arch - x64
    Error: package or namespace load failed for 'docker4seq' in namespaceExport(ns, exports):
    undefined exports: cascStep4
    Error: Loading failed
      Execution stopped
    ERROR: loading failed for 'i386', 'x64'
  • removing 'C:/Program Files/R/R-3.4.0/library/docker4seq'
    Installation failed: Command failed (1)

please see screenshot below
screenshot2.docx

I also ran the docker command: downloadContainers(group="docker"), but got the same error mThank you!running the install_github("kendomaniac/docker4seq") command in R.
I may be mistaken, but the docker4seq downloading and installation steps listed here (http://rpubs.com/rcaloger/280163) seems to work only for linux OS.
Please can someone help ? How can i install docker4seq in windows OS ? Thanks in advance.
@kendomaniac
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kendomaniac commented Jul 12, 2017 via email

@kagningemma
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Dear Sir, thank you for your reply. When I asking the question above, I had already installed Docker Toolbox on Windows 7.
This time, the download was successful, i could download the "docker4seq master" Rpackage in Rstudio installed on my PC. Nevertheless, i am still undergoing the struggles of beginners : I ran the rocker/rstudio container from　the Docker Quickstart terminal, and and typed localhost in the browser, but got no windows pop-up in my google chrome browser. I could neither get a browser tap pop-up when i ran the hello-world container. It seems that i have a firewall or proxy issue, but i am not sure yet. Im Still trying to figure out how to solve the issue.

Thanks

Emma

@kendomaniac
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Hi Emma,
sorry but I cannot follow your explanation.
Lets start something relatively easy to see if the system works on windows:

open the vignette in your browser:
http://rpubs.com/rcaloger/280163
go to:
0.6.1 miRNAseq workflow by line command

download in the desktop this file 130.192.119.59/public/test.mirnaCounts.zip
unzip it in the desktop
open a docker terminal set as working directory test.mirnaCounts
create a file called script.R in the test.mirnaCounts and write inside these lines:

library(docker4seq)

library(docker4seq)
mirnaCounts(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch",
mirbase.id="hsa",download.status=FALSE, adapter.type="NEB", trimmed.fastq=FALSE)

from the docker terminal type:
nohup R CMD BATCH script.R &

the analysis should run in back ground and you should be able to follow it by typing in the terrminal
docker ps
results of what is going on are written in script.Rout

let me know what is happening
cheers
raf

@kagningemma
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kagningemma commented Jul 28, 2017 •
edited
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Hello raf,

I created an R script file (script.R) and ran the command nohup R CMD BATCH script.R & in docker terminal , but got the an error message :
$ nohup R CMD BATCH script.R &
[1] 6964
nohup: ignoring imput and appending output to 'nohup.out'
nohup: failed to run command `R': No such file or directory
[1]+ Exit 127

It also created an empty nohup.out file in the test.mirnaCount directory
image
I changed the extension of the file to script.R.txt and ran the command again, but same error message.

Thanks

@kendomaniac
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I check on my windows
you have to type the full path where R is installed.
In my case C:/R/R-3.2.3/bin/R.exe CMD BATCH script.R &

@kagningemma
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kagningemma commented Jul 29, 2017 •
edited
Loading

this time, i typed the full path where R is installed (the two last commands in the image below) i do not know if that is the expected output.
The two last commands are exactly the same, but different results??
image
It also created a "script.Rout" as well as a "TempFolderID" folder in the R.exe directory
the content of the "script.Rout" file is below
image

I am having issues connecting to docker hub through kitematic, i wrote the question here docker/kitematic#676

@kendomaniac
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kendomaniac commented Jul 29, 2017 via email

@kagningemma
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kagningemma commented Jul 31, 2017 •
edited
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Yes Sir, i did it from the docker quick start terminal. Below are the the contents of the script.Rout file

_**R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(docker4seq)

library(docker4seq)
mirnaCounts(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch", mirbase.id="hsa",download.status=FALSE, adapter.type="NEB", trimmed.fastq=FALSE)

In your system the following version of Docker is installed:
Docker version 17.05.0-ce, build 89658be
creating a folder in scratch folder
It seems that in C:/Program Files/R/R-3.4.0/bin there are not fastq.gz files[1] 1
Warning message:
In dir.create(file.path(scratch.folder, tmp.folder)) :
cannot create dir '\data\scratch\Sat-Jul-29-18-54-49-2017', reason 'No such file or directory'

proc.time()
user system elapsed
0.20 0.06 0.43**_

@kendomaniac
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kendomaniac commented Jul 31, 2017 via email

@kagningemma
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thank you for the good news about your forthcoming windows PC.

So, I created the folder C:/data/scratch, the i ran the /c/"Program Files"/R/R.3.4.0/bin/R.exe CMD BATCH script.R command in docker terminal (in the directory where R is installed, as shown by the 1st command in the image below )

Output:

  • the number 7552 appeared in the docker terminal and
    -an error message from in the script.Rout (1) file

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(docker4seq)
library(docker4seq)
mirnaCounts(group="docker",fastq.folder=getwd(), scratch.folder="C:\data\scratch", mirbase.id="hsa",download.status=FALSE, adapter.type="NEB", trimmed.fastq=FALSE)
Error: '\d' is an unrecognized escape in character string starting ""C:\d"
Execution halted

II. Next i deleted the previous script.R and edited the location of scratch folder in the command your gave changed "C:\data\scratch" to "C:/data/scratch". Then i ran the same command as above (the 2nd command in the image below)

Output:
-2 files were created: script.R (1.2 KB) and tempFolderID (42 bytes) files
The contents of the script.Rout file is below:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(docker4seq)
library(docker4seq)
mirnaCounts(group="docker",fastq.folder=getwd(), scratch.folder="C:/data/scratch", mirbase.id="hsa",download.status=FALSE, adapter.type="NEB", trimmed.fastq=FALSE)

In your system the following version of Docker is installed:
Docker version 17.05.0-ce, build 89658be
creating a folder in scratch folder
It seems that in C:/Program Files/R/R-3.4.0/bin there are not fastq.gz files[1] 1

proc.time()
user system elapsed
0.21 0.01 0.54

The contents of the tempFolderID file is below :

C:/data/scratch/Wed-Aug-02-23-34-02-2017

III. When i ran the nohup R CMD BATCH script.R command (the last command in the image), it still created an empty nohup.Rout file

image

Hopefully when you get your windows PC, a solution shall be found.

@kendomaniac
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kendomaniac commented Aug 2, 2017 via email

@kendomaniac
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kendomaniac commented Aug 2, 2017 via email

@kagningemma kagningemma changed the title Asking for Help : How to install docker4seq in windows? How to install docker4seq in windows? Mar 14, 2021
@kagningemma kagningemma changed the title How to install docker4seq in windows? How to install docker4seq in windows OS Mar 14, 2021
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@kagningemma @kendomaniac