when I run nextflow, I get a .nextflow folder, but I can't find a way to change its location (i.e. it is't -work-dir). How can I change the location of the .nextflow folder?
I have looked at launchDir but it seems that is a read-only implicit variable and cannot be overwritten in the CLI, also, the --launchDir option is only valid for the k8s scope (see original chat in gitter)
I'm using Nextflow 20.10.0 build 5430.
Keeping things neat and tidy is admirable. From this comment, it looks like the only way (without doing crazy things...) is to change to the directory you want your .nextflow cache directory to live and point all other options (i.e. -work-dir, -log etc) away to a separate directory:
If you want .nextflow in dir A and the pipeline work dir in B:
cd A
nextflow run -w B
The .nextflow has to be in the launching
directory to properly maintain the history of the executions.
Related
By default, BlueZ stores its persistent data in /var/lib/bluetooth. This includes controller settings and information about paired devices. However, I'm working in a system where the /var directory is unreliable, so I wonder if there is any way I can change this directory?
I have seen examples where it can be changed during installation, with the "--localstatedir" flag, but I'm looking for a solution that doesn't require reinstallation.
Without reinstalling its not possible. Path is configured at compile time so recompilation and installation is required. You can replace STORAGEDIR macro with string which is read from main.conf to different path at runtime. After modifying these changes you can restart bluetoothd every time you change path then it works.
Question
When building Singularity images using definition files, is there a way to specify the path to a file on the host system relative to the definition file (i.e. independent of where the build command is called)?
Example to Illustrate the Problem
I have the following files in the same directory (e.g. a git repository):
foobar.def
some_file.txt
foobar.def looks as follows:
Bootstrap: library
From: ubuntu:20.04
Stage: build
%files
# Add some_file.txt at the root of the image
some_file.txt /some_file.txt
This works fine when I build with the following command in the directory which contains the files:
singularity build --fakeroot foobar.sif foobar.def
However, it fails if I call the build command from anywhere else (e.g. from a dedicated "build" directory) because it searches some_file.txt relative to the current working directory of the build command, not relative to the definition file.
Is there a way to implement the definition file such that the build works independently of where the command is called? I know that I could use absolute paths but this is not a viable solution in my case.
To make it even more complicated: My actual definition file is bootstrapping from another local image, which is located in the build directory. So ideally I would need a solution where some files are found relative the working directory while others are found relative to the location of the definition file.
Short answer: Not really
Longer answer: Not really, but there's a reason why and it shouldn't really matter for most use cases. While Docker went the route of letting you specify what your directory context is, Singularity decided to base all of its commands off the current directory where it is being executed. This also follows with $PWD being auto-mounted into the container, so it makes sense for it to be consistent.
That said, is there a reason you can't run singularity build --fakeroot $build_dir/foobar.sif foobar.def from the repo directory? There isn't any other output written besides the final image and it makes more sense for the directory with the data being used to be the context to work from.
It's been 14 years since I last worked with svn and appearently I have forgotten everything...
I have an existing web-project, consisting of a bunch of php, html, js and other files in a directory tree on a V-Server. Now I want to take these folders under version control and create a copy on my local machine using svn. So I installed subversion according to these instructions: https://www.linuxcloudvps.com/blog/how-to-install-svn-server-on-debian-9/
Using the already-present apache2.
But now I kinda hit a roadblock. If I try svnadmin create on the existing folder, it tells me that is is not empty and does nothing really. All the questions and answers I find here and elsewhere are either
a) focussing on an already existing folder on the local machine
b) assuming more prior knowledge than I have right now aka I don't understand them.
Is there a step-by-step guide for dummies anywhere on how to do this? Or can anyone tell me in laymans terms how to do this?
I can't believe this case never comes up or that it is really very complicated.
At the risk of failing to understand your exact needs, I think you can proceed as follows. I'll use this terms:
Code: it's the unversioned directory at V-Server where you currently have the bunch of php, html, js and other files
Repository: it's the first "special" directory you need to create in order to store your Subversion history and potentially share it with others. There must be one and there can only be one.
Working copy: it's the second "special" directory you need to create in order to work with your php, html, js... files once they are versioned and it'll be linked to a given path and revision of your repository. At a given time there can be zero, one or many of them.
Your code can become a working copy or not, that's up to you, but it can never become a repository:
$ svnadmin create /path/to/code
svnadmin: E200011: Repository creation failed
svnadmin: E200011: Could not create top-level directory
svnadmin: E200011: '/path/to/code' exists and is non-empty
Your repository requires an empty folder but it can be located anywhere you like, as long as you have access to it from the machine you're going to use in your daily work. Access means it's located in your PC (thus you use the file: protocol) or it's reachable through a server you've installed and configured (svn:, http: or https:).
$ svnadmin create /path/to/repo
$ 😎
Your working copies can be created wherever you need to work with your IDE. It can be an empty directory (the usual scenario) or a non-empty one. The checkout command retrieves your files from the repo and puts them in the working copy so, at a later stage, you're able to run a commit command to submit your new and changed files to the repository. As you can figure out it isn't a good idea to create a working copy in random directories because incoming files will mix with existing files. There's however a special situation when it can make sense: when the repository location is new and is still empty. In that case you can choose between two approaches:
If you want code to become a working copy, you can check out right into in and then make an initial commit to upload all files:
$ svn checkout file://path/to/repo /path/to/code
Checked out revision 0.
$ svn add /path/to/code --force
A code/index.php
$ svn commit /path/to/code -m "Import existing codebase"
$ Adding /path/to/code/index.php
$ Transmitting file data .done
$ Committing transaction...
$ Committed revision 1.
If you don't care about code once it's stored in the repository or you want your working copy elsewhere, you can import your files from code and create a working copy in a fresh directory:
$ svn import /path/to/code file://path/to/repo -m "Import existing codebase"
Adding code/index.php
Committing transaction...
Committed revision 1.
$ svn checkout file://path/to/repo fresh
A fresh/index.php
Checked out revision 1.
I am writing code that creates a folder/file structure in ocaml, and I want to write some tests for it. I'd like to not have to create and delete files each time the tests are run, since they cna be run many times.
What would be the best way to go to mock filesystem? I'd be open to have a filesystem in memory or just mock up functions.
Maybe you could use a Makefile to help you.
For instance make test might start by compiling your program, then create the files and folders required for testing, launching your program, and then cleaning the test folder if need be (at that time, you might also want to check if the state of the test folder is as expected).
On linux:
mount -o size=50m -t tmpfs none ./ramdisk
will create a filesystem in ram, size 50M, mounted to ./ramdisk. Only root can do this. Non-root users can use it. It will show up in df and du. You can clean it by doing umount ./ramdisk.
Creation, usage and removal are working just fine, maybe the root requirement is an obstacle.
I want to change the build dir of team city build agent to:
E://MY_PROJECT_SVN
While installing the build agent I set the same but it diaplays C://buildAgent/work in TeamCity web ui due to which my build fails.
My buildAgent.properties file shows
workDir=E\:\\MY_PROJECT_SVN
And buildAgent.dist.properties file shows
workDir=E://MY_PROJECT_SVN
But I get following error when I run team city
Failed to start MSBuild.exe. Failed to find project file at path:
C:\BuildAgent\work\3ac16e0b4e3af05b\Modules\SIM5.sln
Because of wrong working dir
The buildAgent.dist.properties is indeed just an example, but the solution is something you almost had; you need to put this into the buildAgent.properties:
workDir=E:/MY_PROJECT_SVN
Update:
It should be noted that on TeamCity 7.0 the workDir seemingly can't be on a separate disk; it runs most of the way through the build and then fails. However, using a junction to point from the local (default) folder to the E: drive will work. The tempDir can be pointed to a remote disk though.
The file buildAgent.dist.properties is not used, it is just an example. So don't worry about the contents of that file.
What you have set in buildAgent.properties is what matters. What is happening for you is the agent is reverting to the default location for the working directory.
This means that for some reason it is not able to read or parse the buildAgent.properties file. Make 100% certain that the entire file has no errors in it.
https://confluence.jetbrains.com/display/TCD8/Build+Agent+Configuration
Making any change to this file and saving it should cause the build agent to reboot automatically and reload the new config once it has restarted.
http://blog.jetbrains.com/teamcity/2007/10/configuration-files-editing-without-teamcity-restart/
To build on paul-f-wood's answer:
Teamcity 9.1.6 also has the "feature" where the work directory cannot be on a different drive. I tried several permutations of the temp and work dir, and the only ones that stuck were with the work dir on the same drive as the root teamcity folder. However as paul said, using a junction works like a charm.
cmd: rm C:\BuildAgent\work
cmd: mklink /J C:\BuildAgent\work E:\MY_PROJECT_SVN