problem installing/using seqtk

[azela82]

I am new to seqtk, and installed it following the directions of a previous thread. I am using a MacOSX, and in my terminal typed the following:

$ git clone https://github.com/lh3/seqtk.git
$ cd seqtk
$ make

however, I get the following error message: "-bash: make: command not found"

I would appreciate some advice on what I may be doing wrong or what I can do to use seqtk. Thank you

[vsbuffalo]

Hi azela82,

This is likely because you do not have Xcode installed on your Mac (and if you do, it's because you haven't installed the command line tools). These are some good directions here: http://stackoverflow.com/questions/9329243/xcode-4-4-and-later-install-command-line-tools

[azela82]

Hi Vsbuffalo,

Thank you for your quick reply! Actually, I did install the newest version of Xcode before I installed seqtk because I read somewhere I needed it to work properly. I read through the link you sent, but seems that if I have Xcode it should work?

[vsbuffalo]

You also need to install the command line tools too — see the directions.

[azela82]

Yes, I see now, thank you that worked!

However, now I have another problem. I tried to use the following command to create reverse compliments of a fasta file

seqtk seq -r Undetermined_S0_L001_R1_001.trim.contigs.fasta > out.fasta

however I got the following error: "-bash: seqtk: command not found"

I am also pretty new to using terminal commands, so there may be something very basic that I am doing wrong that I am unaware.

[boulund]

Glad you got the compilation ("make") to work properly!

From the error message you got you can glean that the shell ("bash") cannot find the executable file "seqtk" in your environment. For it to find it (if it's in your current directory) you can type:
$ ./seqtk {commands}
Note the "./" that tell the shell that you want to runt the file called "seqtk" in your current directory (the dot "." represents the current directory).
Hope this helps.
If you want to run seqtk from another directory you might have to write the entire path to the executable to run it, e.g.:
$ /home/azela82/downloads/seqtk_compile_directory/seqtk {commands}

Another way of achieving this is to put the directory in which the seqtk executable exists into your PATH variable. Either put a link to it in your ~/bin directory (if there isn't one in your home directory you can create one) or edit your .bashrc file to include the directory in which your seqtk executable resides to the environment PATH variable. When seqtk is available on PATH you can type:
$ seqtk {commands}
from any directory, like all other installed applications.

[azela82]

Thank you so much for the clear instructions, it worked! =)

[lh3]

Thank boulund and Vince for the help with this issue.

[jibbah]

Hi!

I will post my message here as I also encountered a problem in the compilation. I followed the instructions given on ReadMe file, and I get the following message when entering the command make:
"gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk -lz -lm
seqtk.c:31:18: fatal error: zlib.h: No such file or directory
^
compilation terminated."
I am on Ubuntu 14.04.3 and I have zlib installed.

Thanks for the help!