Question: Error During installation Tophat-Fusion
0
gravatar for debashis.bioinfo
4.0 years ago by
india
debashis.bioinfo0 wrote:

Hello everyone,

During installation of Tophat-Fusion I got this error on the configuration step.

COMMAND:  ./configure --prefix=/usr/local/bin --with-bam=/usr/share/samtools/bin
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... 2.7
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 http://randspringer.de/bam for more documentation.

 

Could you please let me know how to solve this issue? Thanks for your points and tips.

rna-seq software error • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.0 years ago by debashis.bioinfo0

": 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. "

so, did you install this library ?

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k

Just install tophat2, into which the old tophat-fusion functionality has been incorporated. The stand-alone tophat-fusion program has been abandoned.

ADD REPLYlink written 4.0 years ago by Devon Ryan88k
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