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Old 02-18-2013, 10:50 PM   #1
sudheer.svss
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Location: South korea

Join Date: Feb 2013
Posts: 10
Unhappy Tophat 2.0.6 installation error

Dear friends,
I am trying to install Tophat 2.0.6 in fedora 17. I have installed boost 1.40 as suggested by one of r friends in my previous post., I am struck in setting prefixes and paths.,Here im mentioning the procedure I have followed in the installation.
I have entered fedora 17 as root user and created a directory called data then moved boost 1.40, SAM tools, Tophat 2.0.6 into it. I have installed bowite2 and its working.
I have downloaded boost 1.40, and entered sh installation.sh, then ./bjam --prefix=</usr/local> link=static \
runtime-link=static stage install (as mentioned in the Tophat website)
I have downloaded the SAM tools samtools-0.1.18,and copied the libbam.a file in the usr/local/lib, and headers into the /usr/local/include/bam/ as mentioned in the site.
Then I have downloaded the tophat 2.0.6 and run the ./configure with out any prefixes as i want to install it in usr local and the result i got is

Linker flags:
GCC version: gcc (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2)
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr/local
Install eprefix: ${prefix} (im mentioning the last few lines)

then i uses make command which returned error :
make[2]: *** [segment_juncs.o] Error 1
make[2]: Leaving directory `/root/NGS/tophat-2.0.6/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/NGS/tophat-2.0.6'
make: *** [all] Error 2


my bash profile data is
PATH=$PATH:$HOME/bin
PATH=$PATH:$HOME/data/bowtie2-2.0.6/
PATH=$PATH:$HOME/data/perld/bin

im not able to figure it out how to solve this, can u please help me in setting path or so., I m using linux for the first time and learning linux commands, can u please help me.,

Last edited by sudheer.svss; 02-18-2013 at 10:53 PM. Reason: additional information
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