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kendomaniac / docker4seq

Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers.
GNU General Public License v3.0
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How to install docker4seq in windows OS #1

Open kagningemma opened 7 years ago

kagningemma commented 7 years ago

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:/PROGRA~1/R/R-34~1.0/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

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 commented 7 years ago

Dear kagningemma, first I fixed the bug in the github, it should be ok now. please reinstall docker4seq master

second part all containers are linux containers and youneed to install a special type of docker for windows that is in reality a linux virtual machine where docker is run. You need to install https://docs.docker.com/toolbox/toolbox_install_windows/ https://docs.docker.com/toolbox/toolbox_install_windows/ and run R from Docker Quickstart Terminal let me know if you manage. Cheers Raf

Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 Tel. ++39 0116706457 Fax ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calogero@unito.it raffaele.calogero@gmail.com www: http://www.bioinformatica.unito.it

On 12 Jul 2017, at 12:16, kagningemma notifications@github.com wrote:

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 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 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 https://github.com/kendomaniac/docker4seq/files/1141617/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 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.

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kagningemma commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 https://github.com/docker/kitematic/issues/676

kendomaniac commented 7 years ago

Uou start to have a reaction from windows great! Could you please send me what is written in script.Rout Cheers Raf Ps did you run the command nohup R CMD BATCH script.R From the docker quick terminal?

Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone

On 29 Jul 2017, at 11:51, Emmanuel Kagning T notifications@github.com wrote:

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??

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kagningemma commented 7 years ago

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 commented 7 years ago

Hi, You have to create a folder C:\data\scratch and you have to indicate it as parameter of the script scratch.folder:

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)

Let me know what happen :) In September I will have a 32 Gb ram window and I can have a more clear idea of the behavior of docker4seq in windows Cheers Raf

Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone

On 31 Jul 2017, at 05:49, Emmanuel Kagning T notifications@github.com wrote:

Yes Sir, i did it from the docker quick start terminal. Below is 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**_

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kagningemma commented 7 years ago

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:

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 commented 7 years ago

Change in the script \ with /

Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone

On 2 Aug 2017, at 16:47, Emmanuel Kagning T notifications@github.com wrote:

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

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

― You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

kendomaniac commented 7 years ago

In the second script you need to have R starting in the folder where fastq is located

Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone

On 2 Aug 2017, at 16:47, Emmanuel Kagning T notifications@github.com wrote:

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

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

― You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.