Entering edit mode
7.1 years ago
NGS-Newbie
▴
10
Steps:
git clone https://github.com/lh3/seqtk.git
cd seqtk
make
I get the following: gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk -lz -lm
and running seqtk command, I get - -bash: seqtk: command not found
Any ideas, suggestion to get seqtk working on MacOSX.
Thanks!
Do you find a file named 'seqtk' in your current directory? If yes, then your compilation was correct, and you may try running
./seqtkinstead ofseqtk.EDIT: Unix/Linux looks for programs (also called executable) in specific folders, which is defined by a variable named PATH. "." is a shortcut (path) for the current folder. Now to run any program, you have two options: 1) Define in the PATH variable where the program is, or 2) Give
the/full/path/of/the/program. In your case, the current directory is not included in your PATH variable (yous should do that), in absence of which the option (2) works by giving the full path of the program, i.e../seqtkseqtkwould be a logic tag for this question, I've modified your post to add this tag. Make sure to chose sensible tags, as such the developers will easily find your question.Adding your gcc version (
gcc --version) could also be important information.Did the program actually compile? Do you have
macOScommand line tools/XCode installed? Do you see aseqtkexecutable?If you do then it is a matter of doing something like
./seqtk your commandand/or adding the executable to your$PATH.You can ignore that error. I tried the same steps, and the
seqtkexecutable is created, and when I try to run with no parameters, the help screen appears.Thank you all guys! You all are the best!
./seqtk solved the problem!
Make sure you also understand why that solves the problem because this is not specific to seqtk and just a general installation problem of executables.