SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Let's make the SEQwiki even more awesome marcowanger Wiki Discussion 18 04-13-2012 10:49 PM
Can't make Maq nightsun Bioinformatics 1 12-30-2011 08:24 PM
tophat 1.2.0 make error limericksean Bioinformatics 4 04-20-2011 04:16 AM
BWA 'make' error yasu Bioinformatics 3 12-23-2010 03:55 AM
Can't make Maq RockChalkJayhawk Bioinformatics 4 08-24-2009 10:32 AM

Reply
 
Thread Tools
Old 10-19-2011, 09:03 AM   #1
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default Make Clean and Make all not working

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?
qnc is offline   Reply With Quote
Old 10-19-2011, 09:11 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,979
Default

"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).
GenoMax is online now   Reply With Quote
Old 10-19-2011, 09:24 AM   #3
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

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 is offline   Reply With Quote
Old 10-19-2011, 09:24 AM   #4
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

even click throughs on google search for xcode comes up with the same error message btw.
qnc is offline   Reply With Quote
Old 10-19-2011, 09:31 AM   #5
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

Its working now
qnc is offline   Reply With Quote
Old 10-19-2011, 09:38 AM   #6
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

Sorry still problems any advice?
qnc is offline   Reply With Quote
Old 10-19-2011, 09:43 AM   #7
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,979
Default

Do you have the system install DVD handy? Look on there for the Xcode installer.
GenoMax is online now   Reply With Quote
Old 10-19-2011, 09:46 AM   #8
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

No I don't

What about from this site?

http://mac.softpedia.com/get/Develop...le-Xcode.shtml
qnc is offline   Reply With Quote
Old 10-19-2011, 09:55 AM   #9
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,979
Default

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.
GenoMax is online now   Reply With Quote
Old 10-20-2011, 07:26 AM   #10
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Unhappy

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 is offline   Reply With Quote
Old 10-20-2011, 08:12 AM   #11
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

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.
dpryan is offline   Reply With Quote
Old 10-20-2011, 08:18 AM   #12
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,979
Default

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.

Code:
system_prompt> /path_to/BEDtools/bin/intersectBed file1.bed file2.bed
Quote:
Originally Posted by qnc View Post
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??
GenoMax is online now   Reply With Quote
Old 10-20-2011, 08:18 AM   #13
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

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

Is this good?
qnc is offline   Reply With Quote
Old 10-20-2011, 08:21 AM   #14
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

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?
qnc is offline   Reply With Quote
Old 10-20-2011, 10:01 AM   #15
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

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.
dpryan is offline   Reply With Quote
Old 10-21-2011, 05:54 AM   #16
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

Thanks guys having a bit of a mental block here..

Am I suposed to:

Create the following folders inside my BEDTools-v2.13.3/bin folder:
/usr/local/bin/

and then place whole folders with *.cpp , *.h and Makefiles into that?

Will the commands work when I type then then?
qnc is offline   Reply With Quote
Old 10-21-2011, 06:01 AM   #17
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,979
Default

Noooooooooo

Change to the directory where you have the BED files you want to manipulate with BEDTools.

Then use the full path to your BEDTools executables (/path_to/BEDTools-v2.13.3/bin) as I had shown in the example in my previous post (#12 in this thread).

See this link for explanation of UNIX filesystem paths: http://ultra.pr.erau.edu/~jaffem/tut...tem_basics.htm

Quote:
Originally Posted by qnc View Post
Thanks guys having a bit of a mental block here..

Am I suposed to:

Create the following folders inside my BEDTools-v2.13.3/bin folder:
/usr/local/bin/

and then place whole folders with *.cpp , *.h and Makefiles into that?

Will the commands work when I type then then?

Last edited by GenoMax; 10-21-2011 at 06:05 AM.
GenoMax is online now   Reply With Quote
Old 10-21-2011, 06:27 AM   #18
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

That BEDTools-v2.13.3/bin is empty on my system does that mean it wasn't unpacked/complied properly?
qnc is offline   Reply With Quote
Old 10-21-2011, 06:44 AM   #19
qnc
Member
 
Location: London

Join Date: Jun 2010
Posts: 51
Default

Quote:
Originally Posted by dpryan View Post
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.
DO I create this in the BEDTools folder?

i.e. cd to BEDTool then "sudo mkdir -p /usr/local/bin"

And then its an empty folder do I have to put something in it?

Sorry will get this eventually
qnc is offline   Reply With Quote
Old 10-21-2011, 06:52 AM   #20
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,979
Default

Can you look in the "src" directory to see if the files remain there? It is possible that compiled files were not moved to the "bin" directory.


Quote:
Originally Posted by qnc View Post
That BEDTools-v2.13.3/bin is empty on my system does that mean it wasn't unpacked/complied properly?

Last edited by GenoMax; 10-21-2011 at 07:13 AM.
GenoMax is online now   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO