Question: Installation Of Tophat -1.1.4
gravatar for Dayana Janakiraman
3.3 years ago by
Dayana Janakiraman30 wrote:

hi all, am installing tophat and for past 3 days am trying , i could not succeed in it.. the error bug which i get is:

checking for gawk... (cached) gawk
checking for ranlib... ranlib
checking for ar... ar
checking for perl... /usr/bin/perl
checking for bash... /bin/bash
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/local/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-  packages
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 for more documentation.

I have samtools, bowtie installed.and tried all other possible ways up to my knowledge as of:

  • setting new path variables,
  • changing CFLAG to CXXFLAG in tophat/config.h file
  • checked gcc utilities (it is 4.1.1 version) and
  • moved bowtie, bowtie-inspect, bowtie-build to /usr/local/bin and

still cannot solve out..some body please help me out.. thankzzz in advance...

ADD COMMENTlink modified 3.2 years ago by Yifang0 • written 3.3 years ago by Dayana Janakiraman30
gravatar for brentp
3.2 years ago by
Denver, Colorado
brentp17k wrote:

I finally found how to do this. Somewhat confusing instructions are here. You can see that tophat and cufflinks expect samtools (what they call bamlib) libraries and headers to be installed.

More simply,here is a shell script to install samtools stuffs properly so that tophat and cufflinks can use it:


sudo mkdir -p /usr/local/include/bam
sudo cp ${SAMTOOLS}/libbam.a /usr/local/lib/
sudo cp ${SAMTOOLS}/*.h /usr/local/include/bam
sudo cp ${SAMTOOLS}/samtools /usr/local/bin/

you may want to adjust your paths depending on where you have samtools and where the standard place for libraries on your system.

ADD COMMENTlink written 3.2 years ago by brentp17k
gravatar for brentp
3.3 years ago by
Denver, Colorado
brentp17k wrote:

I have had trouble building tophat in recent versions, even after doing as @neilfws suggests (and trying various --with-bam invocations).

They have downloads of both i386 and x64 binaries -- which work for me.

ADD COMMENTlink written 3.3 years ago by brentp17k

sounds very nice..

ADD REPLYlink written 3.3 years ago by Dayana Janakiraman30

thanksss brentp....

ADD REPLYlink written 3.3 years ago by Dayana Janakiraman30

+1 I also had trouble building. It's a shame that TopHat is so difficult to build. I build 100s of tar.gz packages every year without much difficulty but there are inevitably one or two like this one which I end-up forced to install in a black-box which was compiled by someone else.

ADD REPLYlink written 3.2 years ago by Aleksandr Levchuk2.7k
gravatar for Neilfws
3.3 years ago by
Sydney, Australia
Neilfws41k wrote:

The problem, as the error message states, is that the installer cannot find the bam libraries.

This is probably because they are in a non-standard location (such as /usr/lib or /usr/local/lib). You mention that you had to move the bowtie executables to /usr/local/bin, so I suspect that you may have installed bowtie to a non-standard location. Moving the executables is not enough if the libs are in the wrong place.

As the error message suggests, you can specify $BAM_ROOT:

export BAM_ROOT=/path/to/bam/parent/directory

However, I think it might be best to start from scratch: remove what you have installed, unpack the downloaded tarballs, ensure that bowtie is correctly installed in a standard location and take it from there.

ADD COMMENTlink written 3.3 years ago by Neilfws41k

oh.ok.ok.then let me try it..and my fedora is 2.6.2..forgot of mentioning it..

ADD REPLYlink written 3.3 years ago by Dayana Janakiraman30
gravatar for Dayana Janakiraman
3.3 years ago by
Dayana Janakiraman30 wrote:

hi all. i got my tophat working with tophat 1.0.14.tar.gz and am proceeding with RNA-Seq analysis..thanks to all......with

ADD COMMENTlink written 3.3 years ago by Dayana Janakiraman30
gravatar for Yifang
3.1 years ago by
Yifang0 wrote:

Still struggle with the installation of tophat-1.2.0. I have tried everything suggested above, but still not through! Only one thing I was not sure is the PATH settings. Here is what I did: 1. bowtie was successfully installed in $HOME/Downloads/bowtie-0.12.7, and it was running correctly with my real data; 2. tarball of tophat-1.2.0 was downloaded and extracted in $HOME/Downloads/tophat-1.2.0. 3. samtools was also downloaded and installed in $HOME/Downlads/samtools-0.1.13. At least no complain was seen during installation. 4. the libraries needed was copied in other folders created by: 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

By the way, I have added following lines to my /etc/bash.bashrc: export PATH=$PATH:$HOME/Downloads/samtools-0.1.13 export PATH=$PATH:$HOME/Downloads/software/bin/lib:$HOME/software/bin/lib/include/bam

  1. Then I went to tophat-1.2.0 and issued: ./configure --prefix=$HOME/Downloads/tophat-1.2.0 --with-bam=$HOME/software/bin No complain. ...... config.status: creating config.h config.status: executing depfiles commands

-- tophat 1.2.0 Configuration Results -- C compiler: gcc -Wall -m64 -O3 -DNDEBUG C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/home/yifang/software/bin/include GCC version: gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 Host System type: x86_64-unknown-linux-gnu Install prefix: /home/yifang/Downloads/tophat-1.2.0 Install eprefix: ${prefix}

See config.h for further configuration information. Email with questions and bug reports.

  1. but the error showed up when try to make by: :~/Downloads/tophat-1.2.0$ make ---------------------error message--------------------- make all-recursive make[1]: Entering directory /home/yifang/Downloads/tophat-1.2.0' Making all in src make[2]: Entering directory/home/yifang/Downloads/tophat-1.2.0/src' .. juncs_db.cpp:327: instantiated from here ./SeqAn-1.1/seqan/sequence/string_base.h:207: error: no matching function for call to ‘_setLength(seqan::String[?]&, int)’ make[2]: [juncs_db.o] Error 1 make[2]: Leaving directory /home/yifang/Downloads/tophat-1.2.0/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/yifang/Downloads/tophat-1.2.0' make: [all] Error 2

Believe is the setting problem. Please help me out this. Thanks a lot!

ADD COMMENTlink written 3.1 years ago by Yifang0

Please see this related question for the answer: While you're here, take a look around the various questions. This site is a bit different than a standard forum; you've asked your question in an answer field. When you have a new question, please click the 'Ask question' link in the top right of the page. Hope this helps.

ADD REPLYlink written 3.1 years ago by Brad Chapman8.1k
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