I've been stuck on a problem for two days now where the software I'm trying to install will not proceed unless I make a separate user which is non-root.
Keep in mind I'm a big linux noob and not very experienced with the OS.
I make a user called "smrtanalysis" in a group called "smrtanalysis".
I put him in the sudoers file.
I made a folder called smrtanalysis in my home/nick/ directory
I downloaded the software from the PacBio website and put the .run files into this directory I noted above.
I used chmod 777 and chown (to user smrtanalysis) on the directory
noted above, and the .run file
I logged into smrtanalysis user by su smrtanalysis, password, and typed
./smrtanalyis-2.2.0.133377.run
the file runs, but then aborts with the following error message:
We recommend running this script as a designated SMRT Analysis user
(e.g. smrtanalysis) who will own all smrtpipe jobs and daemon
processes.
Current user is 'root' (primary group: root)
Installing as 'root' is currently not supported Switch to the desired
user and restart the install. Aborting installation...
Here is the install documentation:
https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Analysis-Software-Installation-v2.2.0
It seems pretty straightforward but I can't seem to get it working. If you guys look at the install docs, you'll probably be able to tell me what I'm doing wrong.
Thanks for any help!
Regards,
Nick
change
SMRT_ROOT=/opt/smrtanalysis
on
SMRT_ROOT=/home/nick/smrtanalysis
the rest should be easy.
Be very careful installing binaries from internet, make sure you're confident in the source.
Just don't use root for that, you ran the script as root by accident.
(update: pacbio team can help from the github page at https://github.com/PacificBiosciences/SMRT-Analysis/issues as well.)
Related
I wrote Postinst script for changing owner and file permission:
chown -R $(whoami) ~/Desktop/my_file.desktop
chmod 777 ~/Desktop/my_file.desktop
but after installation it does nothing.
I'm really not getting what part of script is wrong. Please tell how to get dynamically username in Postinst script?
Package installation runs as root, unconditionally. There is no concept of an invoking user; indeed, the package installation may happen e.g. before any user accounts exist on the box.
It's extremely unclear what you actually hope to achieve, but it looks like perhaps your package should simply install a script which then performs the task when the user runs it. This will also conveniently create a file which is already owned by the current user, without any chown trickery.
Even if a user exists, there is no guarantee that they have a Desktop directory in their home directory, or that they are currently, or ever, logged in using a GUI.
Finally, whatever you are attempting to do, chmod 777 is wrong and dangerous. You should absolutely not assign write access for everyone, to anything, ever.
(Okay, so there are two or three obscure scenarios related to system administration where this is actually required and useful; otherwise it should probably be technically impossible in the first place.)
I need some help to install the ABySS assembler on PuTTY (virtual Linux) without root permission (as it takes a long time going via IT department etc.).
To be honest I've no idea where to start from, so I'll be very appreciated for step-by-step guide if that is not too much to ask.
Thanks in advance.
If you are referring to the software here, then it should be sufficient to follow the instructions here. Specifically, you should take note of the part labelled To install ABySS in a specified directory:, and specify a directory in your home directory that you have write access to. For example, I might:
mkdir ~/abyss
./configure --prefix=$HOME/abyss
make
make install
Note that I have removed sudo from before make install, so that you are trying to run the installation as a user rather than root. make install will put the software wherever you specified with --prefix.
However, this all depends upon the source code for any libraries upon which ABySS depends existing on your system as well. I expect you will fail at the ./configure step because some library is missing. In this case download the source code for those libraries and tell configure where you have put them (in your home directory), following the example given for Boost on that same page.
I have created quite a few deb files, i have no problems doing that and they all run beautifully. However, if i want to replace a file in users home directory I am unsure on how to do that.
I have tried making a postinst to rsync the files from a predefined location to home directory, but since the postinst file is being run as root ( due to the debian installer running as root ) it is being sent to the root home directory and not the user's home directory....
Here's an example of the deb file contents :
Debian Directory ---> Control File ----> Postint File
usr/share/desktop (directory with files inside)
The postinst file has the sync command to send those files to users home:
#!/bin/sh
rsync -av /usr/share/desktop/ ~/.config/desktop/
The problem is it is sending the files to Root/home... not the default users home :(
I don't have the username of the user since this will be used on many computers with different users, therefore I can't use sudo -u username.
So what do I do? how do i replace files in users home directory from deb install? Any help is much appreciated.
In a Bash script, ~ refers to the current user's home directory. The package installation scripts are always run as root, so that's what "current user" means in this context.
(You could argue that the package installation is probably initiated by a user running su or sudo, but in the general case, you cannot assume this to be the case.)
Modifying user files from a system package appears extremely suspicious in any event. If the need is genuine, this should probably not be approached as a system package installation question in the first place. What are you actually trying to accomplish?
Not only are you violating the basic principle that package management should not meddle with user files; a consequence of this arrangement is that the operation can only be performed once: If the user has installed the package, attempting to install it again does nothing (at least until you uninstall).
A more manageable and predictable approach would seem to be making the package provide this functionality, but leave it to the user to invoke the actual sync (overwriting) script as needed. Perhaps you want to hook it into the desktop startup scripts somehow.
Having said that, sudo exposes the invoking user's identity in $SUDO_USER so you could look for that, and simply fail if it is not set.
As an aside, package scripts should work with dash so you need to avoid bashisms - prefer $HOME over ~, for example.
I managed to find a workaround, although it is not exactly what I was looking for, but here is my solution, at least for now.
#!/bin/sh
#This will move the desktop settings to required folder.
szAnswer=$(zenity --entry --text "Enter your login username\nThis must be entered correctly\n" --entry-text "Enter name of profile to use:")
xfce4-terminal -e "sudo rsync -av /usr/share/Desktop/ /home/$szAnswer/.config/xfce4/"
exit 0
In other words, the user gets asked to enter his username, and the files get copied to that user's home directory. The advantage is that if he does have multiple users, it will use the correct user. The disadvantage is if he enters username wrong, even a spelling mistake, the install will fail.
But it does work, I have tested. If anyone has a better solution I eagerly await your suggestions.
I have spent numerous hours on an issue that has left me puzzled. I am attempting to install Drupal on Linux Redhat using apache, but it will not allow me to pass step 3 due to the fact that sites/default/files is not writable.
I have followed the instructions on Drupal's site, in their install.txt file as well as the instructions of others who have had the same error with no success.
I have granted permissions access all different ways root:root 777, root:apache 777, I have verified that apache is the user running the apache process and I am still stuck.
Note: I was able to complete the install on windows.
Any new ideas?
Okay, so after following directions from both official and non-official web sources, the one thing that was never instructed to do or try was to reboot the application AFTER making permission changes to the files directory. I tried it, and this solved the issue.
This is weird because I've never had to reboot an OS after making permission changes on a directory. Additionally I did restart httpd after each change thinking that would be sufficient. Hopefully this can help anyone else running Redhat 7 with the same issue.
Thanks, TH
I solved this problem by changing the security context of the directory "sites".
My Drupal core files are in: /var/www/html/drupal
Then I applied the command:
chcon -R -t httpd_sys_content_rw_t /var/www/html/drupal/sites/
I'm looking for any advice/intuition/clues/answers on a permission issue that has been plaguing me ever since I switched over to a new Macbook pro. Here's the dilemma. Certain programs copy libraries under /usr/local/lib during install and upon running these programs I get a crash which I believe is related to permission restrictions to files in this folder. I've had errors (can't access files from this path) trying to install plugins for audacity and then tried doing an "ls" under this folder. I immediately get permission denied unless I prefix the cmd with sudo. I've tried owning the /usr/local/lib/audacity folder with my user account and even still I get permissions errors on these files. It's important to note that the problem is not exclusive to Audacity. I've seen the same problem with Polycom video conference software and I've also been unable to run Parallels on this machine. (I haven't traced Parallels to the same issue but I'm betting its related.) I vaguely recall some weird Linux cmd magic I used to use back in the day that would not only grant permission to a user but tweak some low level bits allowing/disabling certain things like execution and I seem to recall the permission thing ran deeper than execution but its been years. I can't recall the detils and I'm wondering if there's something similar on OS X that I'm possibly overlooking. Is there something special about that location and the files there in? Could I have somehow altered my file system in a way tht the files appear different? For what its worth, I seem to be able to use at least one of the programs if I log in as root. I haven't tried with the other programs as I've just discovered the ability. Please help.
It sounds like the folder isn't world executable. Try:
sudo chmod 755 /usr/local/lib
and then you should be able to use ls or anything else in the folder (still won't allow you to write but your user account shouldn't be able to do that anyway)
Found the answer from a coworker buddy. The folder needed to be marked executable.
sudo chmod 755 /usr/local/lib
fixes everything!