Bedtools command not found

sarah_19 · 03-13-2013, 06:41 AM

I have downloaded BamTools 2.17.0 onto my mac OS X 10.5.8 and installed using terminal

I copied all files I want to work with into the bin folder

When in terminal I moved into the bin folder

I can see bedtools

if I manually drag bedtools into the terminal it gives me a description of all the things it can be used for

however anything I type in gets a 'command not found error'

I am trying to run the line
bedtools coverage -hist -abam sample6.bam -b ampfinal.bed >result.txt

when I type this I get:
-bash: bedtools: command not found

cormicp · 03-13-2013, 07:06 AM

Sounds like the folder containing Bedtools might not be in your PATH environment variable

Try ./bedtools coverage -hist -abam sample6.bam -b ampfinal.bed >result.txt when in the bin folder to see if it works.

If it does you can simply add this folder to your PATH and you should be able to call it from any directory.

sarah_19 · 03-13-2013, 09:51 AM

Ah such a simple answer
Thank you so much it worked
Sarah

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
sh: samtools: command not found (Tophat)	lj907	Bioinformatics	3	07-31-2012 11:26 AM
sh: samtools: command not found (Tophat)	lj907	Bioinformatics	4	07-31-2012 10:44 AM
coverageBed: command not found	ibn.adam	RNA Sequencing	6	10-29-2011 03:24 PM
coverageBed: command not found	ibn.adam	RNA Sequencing	0	10-29-2011 12:34 PM
twoBitToFa: command not found	papori	Bioinformatics	11	07-06-2011 05:36 AM

03-13-2013, 06:41 AM	#1
sarah_19 Junior Member Location: London Join Date: Mar 2013 Posts: 2	Bedtools command not found I have downloaded BamTools 2.17.0 onto my mac OS X 10.5.8 and installed using terminal I copied all files I want to work with into the bin folder When in terminal I moved into the bin folder I can see bedtools if I manually drag bedtools into the terminal it gives me a description of all the things it can be used for however anything I type in gets a 'command not found error' I am trying to run the line bedtools coverage -hist -abam sample6.bam -b ampfinal.bed >result.txt when I type this I get: -bash: bedtools: command not found

03-13-2013, 07:06 AM	#2
cormicp Junior Member Location: Dublin Join Date: Jul 2009 Posts: 5	Sounds like the folder containing Bedtools might not be in your PATH environment variable Try ./bedtools coverage -hist -abam sample6.bam -b ampfinal.bed >result.txt when in the bin folder to see if it works. If it does you can simply add this folder to your PATH and you should be able to call it from any directory.

03-13-2013, 09:51 AM	#3
sarah_19 Junior Member Location: London Join Date: Mar 2013 Posts: 2	Ah such a simple answer Thank you so much it worked Sarah