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Old 02-27-2013, 08:48 PM   #1
alittleboy
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Location: USA

Join Date: Apr 2011
Posts: 60
Smile where to copy samtools binary to some directories

I am installing cufflinks on my Mac OS X, and here is the instruction:

http://cufflinks.cbcb.umd.edu/tutorial.html

Under Installing the SAM tools I follow the instructions below

1. Download the SAM tools
2. Unpack the SAM tools tarball and cd to the SAM tools source directory.
3. Build the SAM tools by typing make at the command line.
4. Choose a directory into which you wish to copy the SAM tools binary, the included library libbam.a, and the library headers. A common choice is /usr/local/.
5. Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/)
6. Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
7. Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
8. Copy the samtools binary to some directory in your PATH.

I've done the fist 7 steps, but I am not sure how to proceed with the last step (#8): should I use the command:

sudo cp -a samtools-0.1.18 /usr/local/

or into some other directories? What does the PATH in step 8 indicate? Thanks!
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Old 02-27-2013, 11:17 PM   #2
adrianl
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Location: London

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PATH is a variable containing information on the directories that contain executable programs. If you type echo $PATH into your shell, it will spit the list out. Copy the file into one of those directories. You can also add new folders to your PATH, if you for some reason or another want the binary files in a specific location. You can google your way to how that is done, if youre interested.

//A
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