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.
Trying to get the sidekick image built and having some issues. Is there any documentation other than the README.md file?
My current problem is with getting the JRE requirement working but there are others. The page says "download Oracle JRE and place it inside the working directory. Optionally if you have a company wide distribution url, use that one at a later step." and the help says "Java (JRE) download url or path inside working directory". Have not been able to get this to work.
I went to the JRE link provided and was presented with options to download a rpm file or a tar.gz file. Which is expected (was unable to get either one working)?
It says to place the file in the "working directory" but not sure where exactly. Tried in sidekick folder and in sidekick/jre both without success no matter what I used after the -j command. Is this just the path or should the filename be included as well? Can I get an example?
I'm running this script using my login but noticed the output folder is being created with root user and group. I see no indication that this should be run with sudo. What is the correct way to run this script?
Using debug, I see the function "download if not cached". Can I save these files (JRE, Bamboo jar file, etc.) somewhere so I don't have to worry about downloading them? If so, where should they go? Looks like I might have a problem with the wget to d/l the jar file so would like to just be able to place all these in a folder and be done with it.
It looks like the major problem is the script didn't clean up after itself if it fails. The issue was the first time it failed then that caused subsequent issues as the output folder was already there. Removing this directory between each attempt help.
As for the correct syntax for the -j JRE option I manually downloaded the JRE and placed in a folder called per-build-container/sidekick/stuff/. For the command line it is not just the path but the file name as well (the tar.gz and not the RPM). For my case it was
-j stuff/jre-8u251-linux-x64.tar.gz
Note I also ran the script as sudo. Wasn't stated but seemed to work OK.
Another issue I ran into was the download of the agent jar file. There is a redirect in the wget file that was not working for us. I ended up editing the script and replacing the Altassian based url with the redirected one.
This addresses all the issues I ran into with the initial question.
My situation is I only have execute permission from some folder:
Lets say, I would like to backup entire folder and exclude some folder and files with exclude.txt
Here is path I would like to backup:
/pdf/data/pdfnew/2014
And I only have permission to execute from this folder (main):
/pdf/data/pdfnew/2014/public/main
I put exclude.txt in same folder which I can execute the command (main)
I execute this command in (main folder):
tar -cjvf -X exclude.txt 2014.tar.bz2 /pdf/data/pdfnew/2014
The result is it still included folder that I dont want to backup.
Is there a correct way doing this?
Do you have a user/home directory on that server? You should, so you should just place exclude.txt in your user/homedirectory on that server & run it like this from that directory:
tar -cjvf -X ~/exclude.txt ~/2014.tar.bz2 /pdf/data/pdfnew/2014
The ~/ is a shorthand for your user/home directory so in this case it is explicitly stating, “Read exclude.txt from the user/home directory & write ~/2014.tar.bz2 to the user/home directory.
But you also ask this:
Is there a correct way doing this?
There is never one canonical best way of doing something like this. It is all based on your final/end goal. Nothing more. Nothing less. That said, if I were you I would do it like this instead using the -C option:
tar -cjvf -X ~/exclude.txt ~/2014.tar.bz2 -C /pdf/data/pdfnew/ 2014
The uppercase -C option allows tar to internally change the working directory to /pdf/data/pdfnew/ so you can then create an archive of 2014 without having to have the whole directory tree retained in the backup. I find this is easier to work with because many times I want to backup the contents of a directory but have no use to retain the parent structure. That way the archive is more like a traditional ZIP archive which I find is easer to understand & work with.
I have 10 directories in a AccuRev depot and don't want to populate one directory using "accurev pop" command. Is there any way? .acignore is not suiting to my requirements because in another jenkins build I need that folder. Just want to save time to avoid unnecessary populate of directories.
Any idea?
Thanks,
Sanjiv
I would create a stream off this stream and exclude the directories you dont want. Then you can pop this stream and only get the directories you want.
When you run the AccuRev populate command you can specify which directories to populate by specifying the directory name:
accurev pop -O -R thisDirectory
will cause the contents of thisDirectory to match the backing stream from the time of the last AccuRev update in that workspace.
The -O is for over write and the -R is for recurse. If you have active work in progress the -O will cause that work to be over written/destroyed.
The .acignore is only for (external) files and not those that are being managed by AccuRev.
David Howland
I have found some solutions to this error and tried implementing them but none of which has worked and hope that some here at SO might have a different answer.
I get this error, "Warning! Failed to move file" when I try install modules into my new installation of Joomla here:
http://sun-eng.sixfoot.co.za
Here's some solutions I have tried to no avail:
http://forum.joomla.org/viewtopic.php?f=199&t=223206
http://www.saibharadwaj.com/blog/2008/03/warning-failed-to-move-file-joomla-10x-joomla-15x/
Anyone know of another solution to this please?
Thanks!
Go to Help -> System Info in your administrator backend and check your Directory Permissions tab to make sure everything is writable.
Also make sure your Path to Temp Folder is correct in Site -> Global Configuration.
Finally, check to make sure that the module isn't already installed. It's possible that some files already got copied or something and now your system is having problems overwriting them.
If none of this works, let us know if the error message specifies which file can't be moved. That would help figure out a solution.
In the configuration folder change the temporal folder location to /tmp (public $tmp_path = '/tmp';) or create your own temperate folder and set it to /myowntemp and change the file permission to 777. you are good to go .
This is typically a file permissions issue. If the system cannot write to the tmp directory within Joomla it will give you the "Warning Failed To Move File" error.
The typical solution is to make the directory wide-open, in general a bad practice but a quick fix. You log in to the Linux command line via a terminal (telnet or ssh) session and set the permissions of the directory.
# chmod -R 777 ./tmp
The better option is to find out what user/group the Apache server is running as and assign the permissions accordingly. For example, if Apache is running your site as the myuser:nobody user:group then you can open up write permissions for the group by changing ownership of the tmp folder and making it writable by anyone in the group:
# chgrp -R nobody ./tmp
# chmod -R 775 ./tmp
Security can be a pain to get set correctly if you don't know *nix commands and security settings, so most people just blast a huge hole in the security with chmod 777.
The next thing you'll probably run into is another error message about not being able to update a specific directory. Again, this is a permissions issue and is typically a piece of the file being unzipped into the administrator subdirectory. Depending on whether your installing a component, a module, or a complex plugin with multiple pieces you may need to open up one or more of these directories using the same approach as above. Here is the "blow a big open hole in security" method:
# chmod -R 777 ./administrator/
Or more selectively:
# chmod -R 777 ./administrator/components/
# chmod -R 777 ./administrator/modules/
If you are a linux user then it is very simple to solve. Just type the following command and try again to install plugin/entension.
sudo chmod -R 777 /var/www/html/my_joomla_folder
You can also refer this link for brief information regarding permission of each folder and file.
Cheers!!
In Joomla 3.x you should go to System->System Information to see directory permissions
If one or more directories that are listed are not "writable" then you should change the permission of those directories:
If you are using one of Linux distributions you can use this command
to give the directories read/write/execute permission:
sudo chmod 777 -R address_of_lampp_directory/lampp/htdocs/joomla_directory
I have had a similar issue today and found is was the permissions set on the 'temp folder'. To resolve I changed them to 777 and my plugin installs worked fine!!
Another thing to check is whether you actually have space on the disk. I had this error and discovered that the drive was 100% full. Removing some unused files fixed the problem.
One other thing to try if everything else is not working is to add the following to your .htaccess file:
php_value upload_max_filesize 10M
Make sure 10M covers the size of the file you are uploading - increase it if your file is 12Mb, for instance.
[Source]
This issue was solved like this.
On the configuration.php file change the tmp_path variable according to:
if you site is mysite.azurewebsites.net, the path should looks like
'C:\DWASFiles\Sites\mysite\VirtualDirectory0\site\wwwroot\tmp'
instead of
'C:\DWASFiles\Sites\mysite.azurewebsites.net\VirtualDirectory0\site\wwwroot\tmp'
Refer to the link: http://social.msdn.microsoft.com/Forums/en-US/windowsazurewebsitespreview/thread/2701eadc-9977-46ab-9c56-81a2234bdce4
I did it and every is working for every error problem with OSX, I use OSX version 10.9.2 and get many problems. The way to fix every error is
# cd /Applications
# chmod -R 777 ./XAMPP
some files might not change permission but the problem is gone.
you can create folder and upload fine and picture, including install plugin.