I executed the nvm install script twice in a row by accident in the macOS terminal.
Does it install the updates only or the total packages again?
curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh | bash
Thanks!
The script downloads the total packages again
{ # this ensures the entire script is downloaded #
....
} # this ensures the entire script is downloaded #
(The whole script is based around these brackets, which means that the script downloads it again.)
Related
I've attempted to install Nextflow with command "curl get.nextflow.io | bash" in my Windows system command prompt-bash, but I consistently see this error: Unable to initialize nextflow environment
In parallel, on a remote server, the Nextflow is installed with the same command and I can verify that with ls command. However, when I prepare a sample script (hello.nf), executing it by "nextflow run hello.nf" shows that Nextflow is not characterised.
In any of cases, typing "nextflow info" doesn't recognise nextflow. Is there anyway that I can install Nextflow or have I missed any step? I have also tried with wget, but no success yet.
Thanks in advance!
If you have Windows 10 Version 1903 with Build 18362 or higher, you can use the Windows Subsystem for Linux 2 (WSL 2) rather than having to configure a Linux VM. There's a few hoops to jump through, but this guide (Oct 2021) should be sufficient: Setting up a Nextflow environment on Windows 10
On your remote machine, all you should need to do is to move your nextflow to somewhere in your $PATH. Alternatively, you can just call it with ./nextflow (assuming it is in your current directory).
I wrote a small test project for Singularity Compose, consisting of a small server application, with the following YAML file:
version: "1.0"
instances:
server:
build:
context: ./server
recipe: server.recipe
ports:
- 9999:9999
When I call singularity-compose build, it successfully builds server.sif. Calling singularity-compose up also seemingly works without error, and calling singularity-compose ps results in something that looks just fine:
+ singularity-compose ps
INSTANCES NAME PID IMAGE
1 server 4176911 server.sif
However, the server application does not work, calling my test client results in it saying that there is no answer from the server.
But if I run server.sif directly without compose, everything works just fine.
Also, I tripple checked, my test application listens to port 9999, thus should be reachable from the outside.
What did I do wrong?
Edit:
I also checked whether there actually is any process listening at port 9999 by calling sudo lsof -i -P -n | grep LISTEN, this is not the case. Only when I manually start server.sif without compose it shows me the process listening.
Edit:
I went into the Singularity Compose shell and tried to start the Server application directly in there, just as a test, and it resulted in Permission denied. Not sure if that means anything.
Edit:
I now gave the application execution rights within the shell and called in there, this works. Am now trying to add execution rights in the recipe. If that works, it would be kind of strange, as the executable was build right there, and thus should already have execution rights.
Edit:
I added chmod +x in my recipe both after building Server and before executing it. Doesn't work either.
Also checked whether any bridges exist using brctl show, this is not the case.
Edit: My recipe, adjusted by the input of tsnowlan in his answer below:
Bootstrap: docker
From: ubuntu:20.04
%files
connection.cpp
connection.h
main.cpp
server.cpp
server.h
server.pro
%post
# get some basics
apt update
apt-get install -y wget
apt-get install -y software-properties-common
# get C++ compiler
apt-get install -y g++
apt-get install -y build-essential
apt-get install -y build-essential cmake
# get Qt
apt-get install -y qt5-default
# compile
qmake
make
ls
%runscript
/Server
%startscript
/Server
Again, note that the application works just fine both when compiled and startet normally and when started within a Singularity image (but without Singularity Compose).
The ls at the end of the %post block is used to verify that the Server application was build successfully.
Please share the server.recipe, as it is difficult to identify should be/is happening without it.
Without having that, my guess is that you have a %runscript in your definition file, but no %startscript. When the image is executed directly or via singularity run image.sif, the contents of %runscript determine what happens. To emulate the docker-compose style, the singularity images are started as persistent instances. In this case, the %startscript block determines what runs. If it is empty, it will just start up and sit there doing nothing. This would explain why when run by hand it works but not when using compose.
I'm on a Windows machine using Git 2.7.2.windows.1 with MinGW 64.
I have a script in C:/path/to/scripts/myScript.sh.
How do I execute this script from my Git Bash instance?
It was possible to add it to the .bashrc file and then just execute the entire bashrc file.
But I want to add the script to a separate file and execute it from there.
Let's say you have a script script.sh. To run it (using Git Bash), you do the following: [a] Add a "sh-bang" line on the first line (e.g. #!/bin/bash) and then [b]:
# Use ./ (or any valid dir spec):
./script.sh
Note: chmod +x does nothing to a script's executability on Git Bash. It won't hurt to run it, but it won't accomplish anything either.
#!/usr/bin/env sh
this is how git bash knows a file is executable. chmod a+x does nothing in gitbash. (Note: any "she-bang" will work, e.g. #!/bin/bash, etc.)
If you wish to execute a script file from the git bash prompt on Windows, just precede the script file with sh
sh my_awesome_script.sh
if you are on Linux or ubuntu write ./file_name.sh
and you are on windows just write sh before file name like that sh file_name.sh
For Linux -> ./filename.sh
For Windows -> sh file_name.sh
If your running export command in your bash script the above-given solution may not export anything even if it will run the script. As an alternative for that, you can run your script using
. script.sh
Now if you try to echo your var it will be shown. Check my the result on my git bash
(coffeeapp) user (master *) capstone
$ . setup.sh
done
(coffeeapp) user (master *) capstone
$ echo $ALGORITHMS
[RS256]
(coffeeapp) user (master *) capstone
$
Check more detail in this question
I had a similar problem, but I was getting an error message
cannot execute binary file
I discovered that the filename contained non-ASCII characters. When those were fixed, the script ran fine with ./script.sh.
Once you're in the directory, just run it as ./myScript.sh
If by any chance you've changed the default open for .sh files to a text editor like I had, you can just "bash .\yourscript.sh", provided you have git bash installed and in path.
I was having two .sh scripts to start and stop the digital ocean servers that I wanted to run from the Windows 10. What I did is:
downloaded "Git for Windows" (from https://git-scm.com/download/win).
installed Git
to execute the .sh script just double-clicked the script file it started the execution of the script.
Now to run the script each time I just double-click the script
#!/bin/bash at the top of the file automatically makes the .sh file executable.
I agree the chmod does not do anything but the above line solves the problem.
you can either give the entire path in gitbash to execute it or add it in the PATH variable
export PATH=$PATH:/path/to/the/script
then you an run it from anywhere
I am working on creating an automated unit testing system which will utilise docker to test individual student assignments, written in Python, against a single unit test file.
I have created a website where students can upload their assignments but I'm a little but unsure as to how to get the automation with Docker working.
The workflow looks something like this:
A student uploads an assignment for marking
This is copied to a linux host which contains docker
The file sits here while it waits to be tested
So, say I had twenty student uploading there .py files, named as their unique student numbers, could I:
Create a Docker container which runs Ubuntu and Python
Copy the student file and unit test into this container
Run the unit test
Output the results as a text file
Copy this text file back to my webserver to display the results
Could somebody point me in the right direction to get started with this automation? I'm really just after some help of the Docker side of things, not on copying the files from my webserver to the Docker host.
Thanks.
Yes, it is possible to use Docker for that.
The Dockerfile would look like this:
FROM ubuntu
MAINTAINER xxx <user#example.org>
# update ubuntu repository
RUN DEBIAN_FRONTEND=noninteractive apt-get -y update
# install ubuntu packages
RUN DEBIAN_FRONTEND=noninteractive apt-get -y install python python-pip
# install python requirements
RUN pip install ...
# define a mount point
VOLUME /student.py
# define command for this image
CMD ["python","/student.py"]
Now, you have to build this image with docker build -t student_test ..
To start the script and grab the output you can use:
docker run --volume /path/to/s12345.py:/student.py student_test > student_results_12345.txt`.
The --volume parameter is needed, to mount a student script to the defined mount point. Also, you could start multiple containers at once.
All paths are relative to current working directory.
Checkout the following project
https://github.com/CenturyLinkLabs/buildpack-runner
Uses Heroku buildpacks to create a docker image. Crazy but a neat idea if you get it working.
I use CocoaPods in my project but every time I change something it takes a long time to generate support files, I know it is not something I can control, but just wonder is it something that it generates for sub-libraries, if so, can I save the existing 'support files' and only let it generate the one for newly added libs?
I run 'pod install' every time when I change the Podfile, is it a problem and I should run 'pod setup' instead?
Thanks!
We are working on it:
# AWSiOSSDK is a good test because it has a lot of files
$ find Pods/AWSiOSSDK | wc -l
3001
# and generates a plist with almost 80k lines
$ wc -l Pods/Pods.xcodeproj/project.pbxproj
79766 Pods/Pods.xcodeproj/project.pbxproj
# CocoaPods 0.15.1
$ time pod install --no-integrate --silent
pod install --no-integrate --silent 216,50s user 1,45s system 83% cpu 4:19,68 total
# Modified CocoaPods
$ time dpod install --no-integrate --silent
COCOA_PODS_ENV=development ~/Documents/GitHub/CP/CocoaPods/bin/pod install 8,03s user 0,67s system 55% cpu 15,802 total
More than 4 minutes vs 16s means that the generate support phase should become pretty fast in CocoaPods 0.16.
From Xcodeproj/pull/34
So I can only suggest to wait :-)