I am having difficulty installing something, and wanted to write a detailed list of what I did (including all paths, because I am new to Linux, and have problems reading things unless the full path is listed)
1) I am trying to run a program called "pslToBed". I downloaded it from here (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/).
2) It downloaded a single file called "pslToBed". It looks like a binary file (all jibberish at least), and I saved to the directory /Users/MacOwner/Desktop/rnaseq/pslToBed
3) I did echo $PATH, and got the following
/usr/local/bin:/Users/MacOwner/anaconda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/texbin:/usr/X11/bin:/opt/local/bin:~/bin:/Users/MacOwner/Desktop/bedtools2-2.19.1
4) I selected one path from step (3), namely /usr/local/bin
5) I did: cp /Users/MacOwner/Desktop/rnaseq/pslToBed /usr/local/bin/
6) I added the same line to the bottom of both ~/.bashrc and ~./bash_profile:
export PATH=$PATH:/usr/local/bin/pslToBed
Then, I returned to /Users/MacOwner/Desktop/rnaseq/ and tried to run pslToBed but got an error -bash: /usr/local/bin/pslToBed: cannot execute binary file
I know this may be straightforward to experienced users, but I am stuck, even after searching the internet for several hours now. Do my paths and ideas look correct? And if not, what should I do to get this program running?
First, see what kind of file you have:
file plsToBed
This will print the kind of file (including details about the target architecture).
Next, there's no need to copy the file anywhere before trying to run it. If it's in a particular location and you have cd to that location, then simply:
./plsToBed
will execute it from the current directory.
You shouldn't have been able to copy to /usr/local/bin without being root (I hope you're not doing all this as root).
You don't want to add the name of the file itself to the PATH environment variable; the PATH is a list of directories, not files.
Related
I'm just setting up Kaldi for the first time and going through the tidigits example. However with run.sh, I get:
steps/make_mfcc.sh --cmd run.pl --mem 2G --nj 20 data/test exp/make_mfcc/test mfcc
utils/validate_data_dir.sh: Successfully validated data-directory data/test
steps/make_mfcc.sh: [info]: no segments file exists: assuming wav.scp indexed by utterance.
run.pl: 20 / 20 failed, log is in exp/make_mfcc/test/make_mfcc_test.*.log
Looking at the log files, I see the issue is:
bash: line 1: compute-mfcc-feats: command not found
bash: line 1: copy-feats: command not found
This seems to be a PATH issue, and looking at other forums online seems to confirm this. However I'm not sure how to resolve the PATH issue. I've traced that compute-mfcc-feats and copy-feats commands are called in make_mfcc.sh in the steps folder (supposedly a symlink to the wsj example). Please help!
Path to executables is configured with KALDI_ROOT variable in Kaldi recipes in path.sh script inside the recipe, for example, inside tidigits it is kaldi/egs/tidigits/s5/path.sh. The path specified is relative, so you must run commands from kaldi/egs/tidigits/s5 folder and not from other folder. There could be following problems
You didn't compile Kaldi and binary does not exist in
kaldi/src/featbin
You moved the training folder from kaldi and
you didn't update the KALDI_ROOT variable in path.sh
You run the command run.sh from some other folder, not from
kaldi/egs/tidigits/s5 folder.
Usually you simply need to check contents of path.sh and specify the proper kaldi root there.
I tried to make iverilog command s.t I can run verilog program on my Macbook Air.
After few steps for installing the files, the tutorial told me to type:
export PATH=~/bin:/usr/local/iverilog/bin
It worked in terms of iverilog command, i.e, I can compile .v file. However, normal command like ls, man,etc.
I guess it is the problem of the PATH of the command sets, which means those normal unix command is not located.
Can someone tell me how to fix it and I dont need to export the PATH everytime?
You didn't add your paths to the current paths established by the OS. Instead, you replaced it with your paths. This is what you need to do in order to add paths to your PATH variable:
export PATH=$PATH:~/bin:/usr/local/iverilog/bin
The $PATH part is your current PATH value, which is added (concatenated actually) to the list of new paths you want to add. This is turn is assigned to PATH variable.
To make this additions permanent, you may want to add the above line to the end of your .profile file, or .bash_profile (whatever you have in OS X)
You can also do as this:
http://architectryan.com/2012/10/02/add-to-the-path-on-mac-os-x-mountain-lion/
Which says that you can edit the file /etc/paths and add whatever paths you want to add, one per line, then save that file and your added paths are available. In this case, just remember to use absolute paths. That is, paths starting with / . The first one you use: ~/bin is not an aboslute path. You need to convert it to an absolute path. To do this, remember that ~ is a shortcut to your HOME directory: something like /Users/myloginname. Type echo $HOME to find it out.
I feel like I'm missing something very basic so apologies if this question is obtuse. I've been struggling with this problem for as long as I've been using the bash shell.
Say I have a structure like this:
├──bin
├──command (executable)
This will execute:
$ bin/command
then I symlink bin/command to the project root
$ ln -s bin/command c
like so
├──c (symlink to bin/command)
├──bin
├──command (executable)
I can't do the following (errors with -bash: c: command not found)
$ c
I must do?
$ ./c
What's going on here? — is it possible to execute a command from the current directory without preceding it with ./ and also without using a system wide alias? It would be very convenient for distributed executables and utility scripts to give them one letter folder specific shortcuts on a per project basis.
It's not a matter of bash not allowing execution from the current directory, but rather, you haven't added the current directory to your list of directories to execute from.
export PATH=".:$PATH"
$ c
$
This can be a security risk, however, because if the directory contains files which you don't trust or know where they came from, a file existing in the currently directory could be confused with a system command.
For example, say the current directory is called "foo" and your colleague asks you to go into "foo" and set the permissions of "bar" to 755. As root, you run "chmod foo 755"
You assume chmod really is chmod, but if there is a file named chmod in the current directory and your colleague put it there, chmod is really a program he wrote and you are running it as root. Perhaps "chmod" resets the root password on the box or something else dangerous.
Therefore, the standard is to limit command executions which don't specify a directory to a set of explicitly trusted directories.
Beware that the accepted answer introduces a serious vulnerability!
You might add the current directory to your PATH but not at the beginning of it. That would be a very risky setting.
There are still possible vulnerabilities when the current directory is at the end but far less so this is what I would suggest:
PATH="$PATH":.
Here, the current directory is only searched after every directory already present in the PATH is explored so the risk to have an existing command overloaded by an hostile one is no more present. There is still a risk for an uninstalled command or a typo to be exploited, but it is much lower. Just make sure the dot is always at the end of the PATH when you add new directories in it.
You could add . to your PATH. (See kamituel's answer for details)
Also there is ~/.local/bin for user specific binaries on many distros.
What you can do is add the current dir (.) to the $PATH:
export PATH=.:$PATH
But this can pose a security issue, so be aware of that. See this ServerFault answer on why it's not so good idea, especially for the root account.
I can't figure out how to add a directory to the system path. I found out that the command is something like this:
export PATH=$PATH:/my_path/to/my_dir
Example
I run the terminal in the path where my installation directory is located. In this case I'm talking about Play Framework. And I type:
export PATH=$PATH:/to/play20
It looks like nothing happens. In fact, when I type the command "play" (to execute the framework) I get:
-bash: play: command not found
Can someone please give me a decent step-by-step guide?
Execute the command “/to/play20/play help”. If this gives the expected output (help for the play command), then the executable is available, and the problem is in the shell path. If it does not give the expected output, then the executable is not working.
In the former case, ensure you are running the bash shell. (This is the default for recent versions of Mac OS X, but it may be changed for specific accounts.) To do this temporarily, execute the command “bash”. (When you want to exit the temporary shell, execute the command “exit”.) Then execute the export command again. (When the export command works, it changes the variable without displaying any output, so this is normal.) Check the spelling in the export command carefully.
In the latter case, execute “ls -ld /to/play20/play”. If you get a message that the file does not exist, then the executable is not installed correctly, and I cannot help you further. If the file is present, then it is not executable for some reason. This might be because you do not have permission to access it (especially permission to execute it, marked by “x” in certain places in the initial field of the ls output that may contain hyphens, “r”, “w”, and a few other letters) or that it is a symbolic link to a file that does not exist (indicated by an “l” in the first character of the ls output for the file). Lack of permission can be fixed by the chmod command, assuming you have appropriate permissions for changing permissions on the system. If the file is a symbolic link to another file, you may have a bad installation, or the target file may have permission issues (or be another symbolic link, and so on).
I used addpath(pwd) to get my .m files working in my projects directory. When I close the window and start a new window, the path I just added is gone. But the files still run.
Is it in my path or not? How do I see the directories I have added to my path?
Also, . is the first entry I see from path. Does that mean I don't need to add any directories because it will always search the current directory first?
Thanks.
Basically, yes.
You can add a directory to the search path using addpath(), but as you know, it only exists for the current session and is reset when you restart Octave. If you want a path to survive between sessions, add it to your octaverc, a script file that gets run whenever a new session gets started. Example path to octaverc file is:
C:\Octave\3.2.4_gcc-4.4.0\share\octave\site\m\startup
Since . is in your path by default, Octave will search your current directory for any function files that it needs. Using addpath(pwd) is somewhat useless if you're just going to stay in the same directory. However, there are some cases where it'd be useful, if for example you have a directory that contains your functions, and another one that has the data that you're working on: you could start in the functions directory, do addpath(pwd), and then cd to the data directory while still being able to use your functions.
You can create batch file, which will start Octave with your directory path. Please see example below:
octave-3.6.4.exe -p "C:\MyOctaveDiretory"
-p means addpath()
addpath(pwd); savepath();
Done.
I think there is a bug in Octave (I use version 4.0.3 on Windows). When I create a new file in current path, this can't be called by Octave ("error: 'foo' undefined near line 1 column 1"). If I restart Octave, it works. This addpath(pwd) trick helps me a lot (before I unsuccessfully tried rehash() and cd elsewhere and back again).
If you had the same problem, the reason for the symptom might be:
Start Octave.
Create newfile.m.
Call newfile - fails since Octave did not register its existence.
addpath(pwd) - causes Octave to register it.
Close Octave
Start Octave - now pwd is gone from path, but newfile.m is registered at startup.
call newfile - works
I faced a similar problem in adding path where the path was added by using addpath command directly in Octave GUI (Command Window). The path added was being shown in console window but none of the functions worked.
The problem was solved by changing the path directory from Windows directory to some other direction where OS is not installed.