Make Clean and Make all not working

[qnc]

What am I missing?...

I followed the instruction but all I get is bash: make: command not found I was using Terminal v2.1.2 (-bash) on Mac OSX v10.6.8

******************** Screen dump of what I did ******************
$ curl http://bedtools.googlecode.com/files...v2.13.3.tar.gz > BEDTools.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 906k 100 906k 0 0 372k 0 0:00:02 0:00:02 --:--:-- 374k

$ tar -zxvf BEDTools.tar.gz
x ./._BEDTools-Version-2.13.3
LOTS OF THESE AND FINALY
x BEDTools-Version-2.13.3/data/rmsk.hg18.chr21.bed

$ cd BEDTools-Version-2.13.3

$ ls
LICENSE README.rst bin genomes src
Makefile RELEASE_HISTORY data obj

$ make clean
-bash: make: command not found

$ make all
-bash: make: command not found
******************** End Screen dump of what I did ******************

Any ideas?

[GenoMax]

"Make" program needs to be installed on your machine.

For that you can install "Xcode" dev package. This may be on the OS install DVD if you have it handy. Otherwise you can download it for free from here: http://developer.apple.com/xcode/ You will need to create an account with apple (free).

[qnc]

Registered with Apple

but now I get "Can't connect to application instance" When I use that URL for xcode you gave me.

Any advice?

[qnc]

even click throughs on google search for xcode comes up with the same error message btw.

[qnc]

Its working now

[qnc]

Sorry still problems any advice?

[GenoMax]

Do you have the system install DVD handy? Look on there for the Xcode installer.

[qnc]

No I don't

What about from this site?

http://mac.softpedia.com/get/Development/Compilers/Apple-Xcode.shtml

[GenoMax]

I am able to log into the Mac Dev Center site. It appears to be behaving strangely though. Go back to the xcode URL after your get the error. You may find that you are logged in in spite of the error.

I would advise not to download xcode from elsewhere.

[qnc]

Cool finally got the Xcode and the make file seems to have worked!


Also make "clean and "all" are now working...

Got down to the last command sudo and got this

************ ERROR MESSAGE ***********

BEDTools-v2.13.3$ sudo cp bin/* /usr/local/bin/
cp: directory /usr/local/bin does not exist


************ END ERROR MESSAGE ***********


I did try this command before

***** TYPO RESULTING IN ERROR ********


BEDTools-v2.13.3$ sudo bin/* /usr/local/bin/

WARNING: Improper use of the sudo command could lead to data loss
or the deletion of important system files. Please double-check your
typing when using sudo. Type "man sudo" for more information.

To proceed, enter your password, or type Ctrl-C to abort.

Password:
sudo: bin/*: command not found

***** END TYPO RESULTING IN ERROR ********

I hope my typo didn't destroy that folder??

[dpryan]

I don't think /usr/local/bin exists under OSX by default, so you may have to create it (e.g. "sudo mkdir -p /usr/local/bin") or copy the files to a different directory in your PATH. You didn't destroy anything when you forgot the cp command, you just confused sudo. BTW, you may want to ensure that /usr/local/bin is actually in your PATH (type "echo $PATH" and see if it's listed), otherwise make sure to add it.

[GenoMax]

I do not think you did any damage.

You do not need to strictly follow that last command. All it is doing is putting the executable(s) in the "/usr/local/bin" directory (which is generally in the default PATH on a linux system). On a Mac "/usr/local/bin" is not the default path for executables (do not have a Mac handy to check that out).

You should be able to run the programs by providing full path to program you want to run in your terminal window.

system_prompt> /path_to/BEDtools/bin/intersectBed file1.bed file2.bed

Cool finally got the Xcode and the make file seems to have worked!


Also make "clean and "all" are now working...

Got down to the last command sudo and got this

************ ERROR MESSAGE ***********

BEDTools-v2.13.3$ sudo cp bin/* /usr/local/bin/
cp: directory /usr/local/bin does not exist


************ END ERROR MESSAGE ***********


I did try this command before

***** TYPO RESULTING IN ERROR ********


BEDTools-v2.13.3$ sudo bin/* /usr/local/bin/

WARNING: Improper use of the sudo command could lead to data loss
or the deletion of important system files. Please double-check your
typing when using sudo. Type "man sudo" for more information.

To proceed, enter your password, or type Ctrl-C to abort.

Password:
sudo: bin/*: command not found

***** END TYPO RESULTING IN ERROR ********

I hope my typo didn't destroy that folder??

[qnc]

BEDTools-v2.13.3 $ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

Is this good?

[qnc]

How do I check that its all working?
is there a simple command to see if BEDTools is now executable.

I guess running it from anywhere (no need to move files into 1 folder I can organise my files as I want etc...) would be good so I'll set up that PATH thing.. Any advice on that?

[dpryan]

Seems it's already in your PATH, so you should be able to just create the directory if it doesn't already exist and copy things in.

Leaving the files where they are and running them from there will work fine too, you just have to include the path, as demonstrated by GenoMax. The only downside to this is that it requires more typing.