twoBitToFa: command not found

[papori]

Hey, when i try to convert 2bit file to fasta file by using twoBitToFa prog,
and i get "command not found" message..
why?
thanks in advance..

[dawe]

why?

Either because it is not in your path or because you didn't install it…

d

[papori]

what do you mean : it is not in your path..
where do i have to change?

[papori]

now the error is :
bash: ./twoBitToFa: cannot execute binary file

[dawe]

what do you mean : it is not in your path..
where do i have to change?

the "path" is the set of directories that are "scanned" by default when you need to run an executable. This set is included in the $PATH environmental variable, i.e.

$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin:/opt/local/bin:/Users/dawe/Library/Bioinfo/bin:/usr/local/cuda/bin/:/usr/local/mysql/bin:/usr/local/root/bin

All you have to do is one of these:

• place twoBitToFa into a directory included in $PATH
• add the directory containing twoBitToFa to the $PATH
• run twoBitToFa specifying the full qualified path (i.e. /directory/where/you/have/twoBitToFa)

Also, take a look at this

HTH
d

[dawe]

now the error is :
bash: ./twoBitToFa: cannot execute binary file

Mmm... you probably downloaded the binary for a wrong arch/os. check the output of these commands:

$ uname -ps
$ file twoBitToFa

They somehow have to match (i.e. Linux x86_64 will match ELF 64-bit for GNU/Linux, Darwin will match Mach-O file type)

d

[papori]

sorry, when i am doing:
echo$PATH
i get:
bash: echo/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games: No such file or directory

i was wrong before..

[dawe]

$ echo <SPACE> $PATH

[papori]

Ok, my fault...
so my output is:
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

So, i copy the twoBitToFa to /usr/sbin.
now, when i am doing twoBitToFa hg18.2bit hg18.fa
i have this error:
bash: /usr/sbin/twoBitToFa: cannot execute binary file

Thanks for your patience...

[papori]

when i am doing: uname -ps
i get: Linux unknown

or , when doing: file twoBitToFa
i get: twoBitToFa: ERROR: cannot open `twoBitToFa' (No such file or directory)

[dawe]

Ok, my fault...
so my output is:
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

So, i copy the twoBitToFa to /usr/sbin.
now, when i am doing twoBitToFa hg18.2bit hg18.fa
i have this error:
bash: /usr/sbin/twoBitToFa: cannot execute binary file

Thanks for your patience...

I believe you need to study a little bit more about bash and command line interfaces. Take a look at the Bash Beginner Guide and, please, practice a little bit.
Also, I understand you couldn't know, but /usr/sbin is preferred for system commands available to the super user. You'd better place your custom commands into /usr/local/bin.
About the "file" command... again, you need to specify the fully qualified path.
Lastly, about the impossibility to execute, you may look at this http://tinyurl.com/2uka6tq :-)

d

[salturki]

I got same issue but thanks for dawe's answers I solved it and thought the solution may benefit someone later.

All you need is just download the right version and change the file permissions

first download the right version for your machine from this link (Mac i386 or PPC or Linux 32 or 64)

http://hgdownload.cse.ucsc.edu/admin/exe/

then go to the directory where you downloaded the file in the terminal and write:

chmod 755 twoBitToFa

this will make twoBitToFa file executable.