Compiling cufflinks 0.9.x

[seqmagician]

Hi,

Where do I get bamlib? The http://randspringer.de/bam does not work.

I am trying to compile new cufflinks and tophat and got the folloing message:

./configure
...
checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

Thanks in advance.

[scozza]

This is a problem with TopHat 1.1.0 as well which I have been trying to compile on a Solaris machine all morning. I thought for a moment it might have been BamTools (a C++ API for BAM files) but the version I found does not appear to have the appropriate headers. Has to be something else.

Hopefully Cole will be able to provide an answer.

[Cole Trapnell]

That error message is incorrect and misleading - my apologies. I'll update the build scripts to make it right. In the meantime, I suggest you take a look at the "Getting started" page:

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

Which describes how to install the BAM libraries such that you build can Cufflinks.

[scozza]

Thanks. I should have realized it would be simple.

[dennisg]

hey cole;

I am still getting the error
checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

installing TOPHAT. I have SAMTOOLS installed, but in my home/bin as I do not have permission to install apps on the machine. I looked at the configure and it appears to be a problem with idenfying the version number. I tried using the with-bam option and setting BAM_ROOT to no avail. Help would be really appreciated.

Previous versions of tophat were no problem.

Cheers
Dennis

[dennisg]

Actually, the answer is the same for Tophat as for Cufflinks;

In my case, I just changed the instructions to use /home/user/bin/samtools

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/. (I used /home/user/bin/samtools)
Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/) - /home/user/bin/samtools/lib
Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam) /home/user/bin/samtools/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.

[tospo]

this is still not working for me, trying to install tophat 1.1.0
I copied the samtools binary into $BASE/bin, which is in my PATH
then I created $BASE/bin/lib
and copied libbam.a into this folder
then I created $BASE/bin/include/bam
and copied all headers (*.h) into that folder.

I still get


checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

when I configure tophat.

I tried to set BAM_ROOT to any of the above folders but that didn't make a difference either. http://randspringer.de/bam doesn't exist.

[ozs2006]

Diffculty in installing topHat/Cufflinks

Cufflinks and topHat are wonderful softwares, I can't wait to use them on my RNA-seq analysis.
I tried to install topHat from source code.
I followed your instructions, and also install samtools again.
It seems to me that libbam.a never created in my samtools directory, so I cannot add it to the topHat/cufflinks path.

[tospo]

it's working for me now. Turns out that I had to use the --with-bam option and I was confused by the error message which said not to use this option.
Anyway, here is what I did (basically the same as posted above):

I'm installing in $HOME/software
the executable will go in $HOME/software/bin

mkdir $HOME/software/bin/lib

mkdir -p $HOME/software/bin/include/bam

Copy files from the samtools source into those new directories. I had downloaded and untar'ed samtools in $HOME/downloads:

cp $HOME/downloads/samtools-0.1.8/libbam.a $HOME/software/bin/lib
cp $HOME/downloads/samtools-0.1.8/*.h $HOME/software/bin/include/bam

wget [url]http://tophat.cbcb.umd.edu/downloads/tophat-1.1.0.tar.gz[/url]
tar -xzvf tophat-1.1.0.tar.gz
cd tophat-1.1.0
./configure --prefix=$HOME/software --with-bam=$HOME/software/bin
make
make install

now it's working fine.

[ozs2006]

I eventually downloaded samtools 1.0.7a and followed your instructions, then I downloaded binary of tophat.
It work (as it seems from running the test_data) .
thank you very much