Installing Tophat Fusion

[Kwafelenge]

Hi All,
I thought I was good at following directions.. I've written some code myself, all in bash shell, for running and interpreting some basic sequence alignments with megablast and BWA.

But want to check out tophat fusion.

I've gotten what I thought were all the pieces (samtools, bowtie) installed, and made some new folders and copied some files. But upon configure, I'm getting the message that something is wrong. I don't know whether I've given tophat fusion what it's looking for. Anyone with some experience know what's going on?

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My details:
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b1a:bam] pwd
/ifs/scratch/c2b2/rr_lab/shares/samtools-0.1.18/include/bam
b1a:bam] ls
bam2bcf.h bam_endian.h bam.h bgzf.h errmod.h faidx.h kaln.h khash.h klist.h knetfile.h kprobaln.h kseq.h ksort.h kstring.h razf.h sam.h sam_header.h sample.h
b12b:tophatfusion-0.1.0] cd /ifs/data/c2b2/rr_lab/jbr2143/Programs/tophatfusion-0.1.0
b12b:tophatfusion-0.1.0] ls
aclocal.m4 annotation AUTHORS ax_bam.m4 ax_check_zlib.m4 build-aux ChangeLog config.h.in config.log configure configure.ac COPYING include INSTALL lib Makefile.am Makefile.in NEWS README src THANKS
b12b:tophatfusion-0.1.0]
b12b:tophatfusion-0.1.0] ./configure --prefix=/ifs/data/c2b2/rr_lab/jbr2143/Programs/tophatfusion-0.1.0 --with-bam=/ifs/scratch/c2b2/rr_lab/shares/samtools-0.1.18/include/bam/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
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/bin/python
checking for python version... 2.5
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.5/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python2.5/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 http://randspringer.de/bam for more documentation.

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Info in the README file:
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TopHat requires the Samtools package (http://samtools.sourceforge.net/)
in order to generate and handle the compressed, binary alignment files (BAM).
The --with-bam=<bam_prefix> option of the configure script expects the
following subdirectories and files:

<bam_prefix>/include/bam/*.h (all the header files from Samtools)
<bam_prefix>/lib/libbam.a (obtained by compiling Samtools)

At the time of this writing the Samtools package does not have an
install routine the user will have to explicitly create the above
directory structure (./include/bam/ and ./lib) and copy the required
Samtools files as indicated (the header files and libbam.a)



Regards,
Jonathan

[Jon_Keats]

The only thing I can guess is it might want the include directory one level back from the executable directory. These instructions have worked for tophat on Mac and Linux and tophat-fusion (Linux) (http://seqanswers.com/forums/showthr...?t=4589&page=3) for tophat-fusion, based on my experience I'd recommend the pre-built binary for your OS. There are a couple of bugs in that package...