使用tospo的方法解決了 cufflink 安裝時候，出現(xiàn)的如下問題：
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.
解決方法如下：
tospo
10-26-2010, 05:42 PM
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 $HOME/software/bin/include/bam
注意：在$HOME/software/bin/目錄下操作可以成功！
之前錯誤的原因在是我/home/zhanglei/.local/目錄下操作。
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seqmagician
10-05-2010, 12:42 AM
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
10-05-2010, 01:06 AM
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
10-05-2010, 01:07 AM
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
10-05-2010, 01:11 AM
Thanks. I should have realized it would be simple.
dennisg
10-05-2010, 11:35 AM
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
10-05-2010, 11:46 AM
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
10-20-2010, 12:55 AM
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
10-26-2010, 05:01 PM
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. :confused:
tospo
10-26-2010, 05:42 PM
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 $HOME/software/bin/include/bam
wget http://tophat.cbcb.umd.edu/downloads/tophat-1.1.0.tar.gz
tar -xzvf tophat-1.1.0.tar.gz
cd tophat-1.1.0
./configure --prefix=$HOME/software --with-bam=$HOME/software/bin
make
make install
now it's working fine.
ozs2006
10-27-2010, 11:31 PM
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
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