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使用tospo的方法解决了 cufflink 安装时候，出现的如下问题：
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:///bam for more documentation. 解决方法如下： tospo 10-26-2010, 05:42 PM 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/目录下操作可以成功！ 之前错误的原因在是我/home/zhanglei/.local/目录下操作。 SEQanswers > Bioinformatics > Bioinformatics > Compiling cufflinks 0.9.x View Full Version : Compiling cufflinks 0.9.x seqmagician 10-05-2010, 12:42 AM Hi, Where do I get bamlib? The http:///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:///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./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:///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:///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:///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 $HOME/software/bin/include/bam wget http://tophat.cbcb./downloads/tophat-1.1.0.tar.gz tar -xzvf tophat-1.1.0.tar.gz cd tophat-1.1.0 ./configure --prefix=$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 vBulletin? v3.8.6, Copyright ?2000-2015, Jelsoft Enterprises Ltd.
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来自： panhoy > 《Software》
