Hi everyone
Now I have installed tophat on mac64bit,but I have some question.
I download tophat-1.31 Mac OS X x86_64 binary,and it doesn't need to compile.
The following is maual of tophat
My question is tophat 64 bit doesn't need to compile.
How do I ./configure --prefix=..../../.
And when I run tophat,it shows the error
If anyone know how to solve
Please tell me.
Thanks
Now I have installed tophat on mac64bit,but I have some question.
I download tophat-1.31 Mac OS X x86_64 binary,and it doesn't need to compile.
The following is maual of tophat
You will also need the samtools program in your PATH, and if you plan to compile Tophat from source you should also install the SAM tools package, by following these steps:
Download the SAM tools
Unpack the SAM tools tarball and cd to the SAM tools source directory.
Build the SAM tools by typing make at the command line.
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/.
Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/)
Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
Copy the samtools binary to some directory in your PATH.
To install TopHat, unpack the tarball and change to the package directory as follows:
tar zxvf tophat-1.2.0.tar.gz
cd tophat-1.2.0/
Now build the package:
./configure --prefix=/path/to/install/directory/
Note: If you copied the SAM tools library and header files to someplace other than /usr/local/, you may need to supply the --with-bam configuration option. For example, if you placed the libbam.a files in /opt/biotools/lib/ and SAM tools .h files in /opt/biotools/include/bam/ then the configure command will become something like this:
./configure --prefix=/opt/biotools --with-bam=/opt/biotools
(in this example tophat and its modules will be installed in /opt/biotools/bin/ directory)
After the configure script finishes successfully, build the Tophat package:
make
Finally, install TopHat:
make install
This will install tophat and its modules into /path/to/install/directory/bin directory. You may want to add that directory to your shell's PATH if it's not there already.
Download the SAM tools
Unpack the SAM tools tarball and cd to the SAM tools source directory.
Build the SAM tools by typing make at the command line.
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/.
Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/)
Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
Copy the samtools binary to some directory in your PATH.
To install TopHat, unpack the tarball and change to the package directory as follows:
tar zxvf tophat-1.2.0.tar.gz
cd tophat-1.2.0/
Now build the package:
./configure --prefix=/path/to/install/directory/
Note: If you copied the SAM tools library and header files to someplace other than /usr/local/, you may need to supply the --with-bam configuration option. For example, if you placed the libbam.a files in /opt/biotools/lib/ and SAM tools .h files in /opt/biotools/include/bam/ then the configure command will become something like this:
./configure --prefix=/opt/biotools --with-bam=/opt/biotools
(in this example tophat and its modules will be installed in /opt/biotools/bin/ directory)
After the configure script finishes successfully, build the Tophat package:
make
Finally, install TopHat:
make install
This will install tophat and its modules into /path/to/install/directory/bin directory. You may want to add that directory to your shell's PATH if it's not there already.
How do I ./configure --prefix=..../../.
And when I run tophat,it shows the error
[Wed Jul 13 16:28:25 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Wed Jul 13 16:28:25 2011] Preparing output location ./tophat_out/
[Wed Jul 13 16:28:25 2011] Checking for Bowtie index files
[Wed Jul 13 16:28:25 2011] Checking for reference FASTA file
[Wed Jul 13 16:28:25 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jul 13 16:28:25 2011] Checking for Samtools
Error locating program: samtools
-----------------------------------------------
[Wed Jul 13 16:28:25 2011] Preparing output location ./tophat_out/
[Wed Jul 13 16:28:25 2011] Checking for Bowtie index files
[Wed Jul 13 16:28:25 2011] Checking for reference FASTA file
[Wed Jul 13 16:28:25 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jul 13 16:28:25 2011] Checking for Samtools
Error locating program: samtools
Please tell me.
Thanks
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