lftp can get the files which symbolic links point to, but can it get these files if they are in directories represented by symbolic links? For example, I am looking to get files at
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Acinetobacter_nosocomialis/all_assembly_versions/GCA_000162375.2_Acin_sp_RUH2624_V1/
where /GCA_000162375.2_Acin_sp_RUH2624_V1/ is a symbolic link to a directory.
I tried adding set ftp:list-options "-La" to ~/.lftprc, ~.lftp/rc, and /etc/lftp.conf.
This is the command I am using:
lftp -c 'open -e "mirror -c -p --no-empty-dirs -I *.gz /genomes/genbank/bacteria/Acinetobacter_nosocomialis/ ~/ncbi_bacteria_mirror" ftp.ncbi.nlm.nih.gov'
This command DOES work on ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Pseudomonas_sp._URMO17WK12_I11/all_assembly_versions/
where /all_assembly_versions/ is not a symbolic link. It does not however recursively follow the symbolically linked directories contained within and get the files from those directories, which I would like for it to do if possible.
Resolving the file name to the file on disk and thereby resolving symbolic links is done at the server. Thus there is no need for the ftp client to resolve these links, which means it will not even attempt it by trying to guess the format of the directory listing.
I am not sure I understand the question, and the answer is hidden in it: the -L flag is what you want.
Quoting lftp's man page:
-L, --dereference download symbolic links as files
That's really it!
Related
I have a rule whose output files are symbolic link files. Even though the link files are being made, Snakemake exits with a MissingOutputException and lists the output files as being missing. If instead of making a symlink with "ln -s" I copy the files with "cp -p" it works. I tried increasing the --latency-wait but it made no difference.
Sounds like you are using relative path for source file when symlinking. Use absolute path.
Snakemake sees broken symlinks as missing output.
Given a file somewhere in the file system, can I find out which symbolic links exists that point to that file?
The purpose of this would be to determine if a file can be successfully deleted, or if deleting the file would leave behind a bunch of dead symbolic links.
If you do an "ls -l" in a directory that contains a file which is a symbolic link, the ls command will show you where the link goes. I'm looking for the reverse of that, which is getting a list of symbolic links around the file system which point to a specific file.
For example:
$ ls --optionToFindSymLinks? ./thefile.txt
/home/user/dir/file.txt -> ./thefile.txt
/home/otheruser/dir/file2.txt -> ./thefile.txt
2 symbolic links found
I realise that unmounted file systems might contain links that I won't be able to find, but this would not be a problem in my case.
Edit: Attempt at clarification
There is no reverse search. You have to do the work yourself. Get a list of all the symbolic links in your system and check which of them point to the file you are interested in.
I need my client to be able to see the file in the directory they are allowed on. So I soft link the directory they are allowed on but can't see the files inside even tho they have the right (rwx).
ex:
/home/user1/project1.link/(couple of files)**
/clients/client_shamwow/project1/(couples of files)
**: Can't see the files.
This is the line I used:
ln -s /clients/client_shamwow/projet_prod /home/user1/projet_prod
is there something wrong that I am doing so they can't see the files in project_prod or I should use something else?
Your command doesn't match your example, but I assume you mean /home/user1/project1.link is a soft (symbolic) link, and when you run ls it lists just that name, rather than the contents of the directory the link points to. If that's the case, add the -L option to your ls command.
ls -lL /home/user1/project1.link
The man page says:
-L, --dereference
when showing file information for a symbolic link, show information
for the file the link references rather than for the link itself
Another way is simply to append /. to the end of your command, as in
ls -l /home/user1/project1.link/.
If that doesn't answer your question, I think you need to be more clear, and perhaps clean up the inconsistencies in your question. Even show some real output and the commands you ran.
Solved. No idea what happend. I just recreated the link the exact same way I did before and now I am able to see AND modify the files as the user1 w/o him being able to go anywhere else than what is in the folder project_prod. Thx for your time :)
When I type ls -la to list all the files, I see this:
11 Jul 9 12:04 libcrypto.so -> libcrypto.so.0
I tried to change the name of libcrypto:
mv libcryto.so libpmcrypto.so
And now it shows:
11 Jul 9 12:04 libpmcrypto.so -> libcrypto.so.0
Does that affect anything? And what does the arrow mean?
The file in question is a symbolic link. This is conceptually similar to the idea of a shortcut, but it appears to be the real file if you use it (Open it, copy it, etc.). The symbolic link is another name that "points to" the real file. When you do ls -l it also shows you which file is pointed to by the link. Renaming the link has no effect on the original file, but may break things that rely on the link name, just as with any other file name. Deleting the link just removes the pointer, and has no effect on the original file. Deleting the original file will leave the link in a "broken state" where the link points to nothing.
Edit
You can't really edit what symbolic links point to. You can delete them with rm and then recreate them with the ln -s command. Take a look at the man pages for more information.
-> means libpmcrypto.so is a Symbolic link and the information stored in libcrypto.so.0 is accessible through the libpmcrypto.so file.
How to create a symbolic link:
ln -s [TARGET DIRECTORY OR FILE] ./[SHORTCUT]
for example:
ln -s /usr/local/apache/logs /home/el/logs
If you delete the soft link itself (/home/el/logs), the file (/usr/local/apache/logs) would still be there.
How to find symbolic links:
find ./ -type l
read man ln for more information on links.
ls -la will display files pointing to module using symbolic links
For example in your library directory you have file pointing to the .so files (shared object).
This means it does not need to be recompiled. You have no easy way of telling how files are linked.
Yes that does changes something, in fact you shouldn't change a shared library because when a 3rd-party program tries to call libcryto.so its not going to be there any more.
But if you're sure you want to change the name, I would recommend you to call nautilus in superuser mode:
sudo nautilus /THE/FOLDER/WHERE/YOUR/FILE/IS
And edit it manually, by adding .0 to the end of the symlink name. You're changing part of its name so whenever a program tries to call it, its not going to be able to locate it.
I currently have rsync working well. It copies all my files from one directory to another directory. The only thing is it is physically copying the files.
I have a lot of large files that I don't want to have a duplicate of all the files. I just want to create a symbolic link in the new directory so that I can serve the data on a webpage. The source directory has some scripts and files I don't want the public to see. I'm moving the safe data to the web root (destination).
What I would like rsync to do is any new files in the source directory would create links into the destination. That way I am not using up my hard drive space like I currently am doing. What I have works perfect except for doing the symbolic link aspect to it. Is there a way to have rsync track and create symbolic links?
rsync -aP --exclude="file.sql" --exclude="*~" --exclude=".*" --exclude="*.sh" . ${destination}
It's not a symlink, but you might be able to work with --link-dest=DIR. It creates a hard link which will create a new name for the same file. This will behave similarly to a softlink as long as:
Both files are on the same filesystem
You don't plan to delete the original and not the copy (the symlink would break but a hard-link won't)
You don't have anything explicitly checking to see if it's a softlink
You could use cp -aR -s (Linux or FreeBSD) or cp --archive --recursive --symbolic-link (Linux) to create symbolic links to the source files in the destination directory instead of copies. Note that -s is non-standard.
Can lndir be useful to you. According to manual it creates a shadow directory of symbolic links to another directory tree.
I think master_delivery is probably the best tool for this. With the already introduced --link-dest option of rsync, files which are not the same will be copied. If you don't mind the situation where copies and hardlinks are mixed, you can use rsync, but if you want to eliminate duplicates completely, use master_delivery.
Usage is:
gem install master_delivery
master_delivery -m <path_to_master> -d <path_to_delivery_root>