I downloaded a "directory".tar.gz, extracted and unzipped the file to obtain "directory".
The installation files for this directory, were to run the make command in cygwin, to compile and pull out the files of the directory, which were written in C.
I attempt to run a command in cygwin, pfunc, which is a command supposed to be available after compiling and performing make, but cygwin says command not found.
I'm completely new to unix and cygwin.
The problem is that pfunc, if it exists, is not on your path.
The first step is to see if pfunc actually exists and if so, find out where. find / -xdev -name pfunc will give you the location of all files named pfunc. Obviously, if pfunc doesn't exist, you have another problem on your hands.
Next, you'll want to add this path to your bashrc. You can do that with:
echo "export PATH=$PATH:<the/path/find/gave/you> >> ~/.bashrc
Finally, you need to update your path in the current shell with source ~/.bashrc
K, I figured it out, there was a problem with the implementation of the program on cygwin, and for some reason find -name ....etc couldn't find the file. However, I found the location and reset the path to find the .exe file. Now everything looks good! thanks again!
Related
I just installed CD-HIT and followed these instructions:
Installation
Most CD-HIT programs were written in C++. Installing CD-HIT package is very simple:
download current CD-HIT at http://bioinformatics.org/cd-hit, for example cd-hit-2006-0215.tar.gz
unpack the file with ” tar xvf cd-hit-2006-0215.tar.gz --gunzip”
change dir by “cd cd-hit-2006”
compile the programs by “make”
you will have all cd-hit programs compiled
I followed these steps and indeed .exe files were made:
cdhit.c++ cdhit-est-2d.c++ clstr_select_rep.pl
cd-hit.exe cd-hit-est-2d.exe clstr_size_histogram.pl
cdhit.o cdhit-est-2d.o clstr_size_stat.pl
cdhit-2d.c++ cd-hit-para.pl clstr_sort_by.pl
cd-hit-2d.exe cdhit-utility.c++ clstr_sort_prot_by.pl
cdhit-2d.o cdhit-utility.h clstr_sql_tbl.pl
cd-hit-2d-para.pl cdhit-utility.o clstr_sql_tbl_sort.pl
cdhit-454.c++ ChangeLog clstr2tree.pl
cd-hit-454.exe clstr_cut.pl clstr2txt.pl
cdhit-454.o clstr_list.pl clstr2xml.pl
cd-hit-auxtools clstr_list_sort.pl doc
cdhit-common.c++ clstr_merge.pl FET.pl
cdhit-common.h clstr_merge_noorder.pl license.txt
cdhit-common.o clstr_quality_eval.pl make_multi_seq.pl
cdhit-div.c++ clstr_quality_eval_by_link.pl Makefile
cd-hit-div.exe clstr_reduce.pl plot_2d.pl
cdhit-div.o clstr_renumber.pl plot_len1.pl
cd-hit-div.pl clstr_rep.pl psi-cd-hit
cdhit-est.c++ clstr_reps_faa_rev.pl README
cd-hit-est.exe clstr_rev.pl usecases
cdhit-est.o clstr_select.pl
However when I typ: cd-hit-est in the cygwin command line, it will say: -bash: cd-hit.exe: command not found. I'm not able to figure out why this is happening. Even when I'm in the folder were the .exe files are located it still will give the same error.
When you try to run command without a path, bash tries to find the command name in each directory from the PATH environment variable.
Usually current directory "." is not in the PATH so you have to run command adding absolute or relative path before command name:
./cd-hit.exe
or
/absolute/path/to/your/cd-hit/program/cd-hit.exe
If you want to permanently run command cd-hit.exe from anywhere, just add the directory where cd-hit was compiled to any existing auto-loaded bash profile files:
.profile
.bashrc
.bash_profile
like
PATH=$PATH:/absolute/path/to/your/cd-hit/program
export PATH
Can anyone tell me where my file may have gone after this command?
The file I'm missing is stats.cpp
And what is the correct command to move it from directory prog3a to prog3c?
Thank you.
Since you did not post the actual command you used I cannot tell you what happened to the file. What I can say is that unless you used the rm command, the file is not gone. Probably got its name changed if you cannot find it or it got moved somewhere else other than the intended destination.
The correct command you should use is
mv prog3a/stats.cpp prog3c/stats.cpp
This command should be run in the directory where both prog3a and prog3c folders exist (cd to it before running the command. This is assuming they're both inside the same directory).
A more specific answer can be provided if you tell us which command you initially ran specifically and the full paths of each folder.
I am trying to execute a Makefile script and my Mac complains about 7zcat, although I already have 7z installed.
/bin/sh: 7zcat: command not found
Any thoughts on what's missing on my system? Thank you!
I have never used 7zcat before.
However, it looks like it needs to be installed on your system.
https://github.com/essentialkaos/7zcat
Also, after you download install 7zcat you have to give it execute permission with chmod. Finally, you have to execute it by calling its full path for example if you installed it to the directory you are in you would run ./7zcat file.7z or you would add the path to the file to your environment's $PATH variable.
I hope this helps. You might have to do some more research though.
When you open a Terminal window and type 7zcat and hit enter, what happens? Same message? Well, if you cannot use it, why should make be able to use it? Where and how have you installed 7z? Is the folder with the 7z binaries in your PATH? Since if it isn't, of course the command won't be found.
When the system shall run a command, it will search for this command in the directories stored in the PATH variable. Execute echo $PATH in terminal and you will get a colon separated list of directories; only these directories are searched for binaries. So either you must move your binaries to one of these (or put a symlink to one of these) or add the directory with these binaries to the PATH.
Yet there is no official 7z command line installer for MacOS, which brings me back to the original questions "Where and how have you installed 7z?" And are you sure that whatever you installed even includes a 7zcat?
I am very new to bash and using .sh files. I am trying to run the program aescrypt by calling it in a .sh file as follows (aescrypt is in the same directory as the .sh file) :
./aescrypt -e -p password file.txt
It throws the following error:
./aescrypt no such file or directory
Am I doing it wrong?
ps- I realy don't want to add it to the PATH variable as I will be using this on more than one computer that resets every day.
The location of the script is irrelevant. The thing that matters is the working directory of the process executing the script. The simplest solution really is to add aescrypt to a standard location like /bin or /usr/bin. If neither of those is acceptable, perhaps /usr/local/bin is an option. Otherwise, just use the full path of aescrypt in your script. Either hard code it, or if it is in the same directory as the script, try:
$(dirname $0)/aescrypt ...
(Note that hardcoding is more reliable, but less flexible. If you move the executable, the script will break. But using dirname will break if the script changes directory during execution.)
how about if you call the program like ./aescrypt.sh, thats the way to call an .sh programm througt the terminal
First off all, you have also to change the permissions of the file to make it executable, the way to make that is to write in the terminal, the command:
sudo chmod 765 aescrypt.sh
For that you have to be located where the file is
I just made a .c file and compiled it with gcc in the terminal on OS X 10.8.2.
My syntax was gcc -o <filename> <sourcefile> and that was fine. Now I see I have an executable and file <filename> tells me as such, but I'm not sure how to actually run it beside double clicking the icon, /lame. When I try running the executable by just typing I get command not found, but I thought it was executable...?
Thank you.
EDIT: I"m so stupid, it was just open <filename>
Unix will only run commands if they are available on the system path, as you can view by the $PATH variable
echo $PATH
Executables located in directories that are not on the path cannot be run unless you specify their full location. So in your case, assuming the executable is in the current directory you are working with, then you can execute it as such
./my-exec
Where my-exec is the name of your program.
To run an executable in mac
1). Move to the path of the file:
cd/PATH_OF_THE_FILE
2). Run the following command to set the file's executable bit using the chmod command:
chmod +x ./NAME_OF_THE_FILE
3). Run the following command to execute the file:
./NAME_OF_THE_FILE
Once you have run these commands, going ahead you just have to run command 3, while in the files path.