TopHat "configure: No such file or directory"

[norafar]

Hello All,

I am a newbie and trying to install TopHat, but am receiving configuration error. I looked through the site and there are several similar errors but the solutions seem to be not applicable in my case.

Here is what I have done (OSX 10.8.3)

1) I have downloaded boost (with default prefix of /usr/local)
2) I had previously downloaded samtool; so:
3) copied libbam.a to the /usr/local/lib/
4) copied the headers (*.h) to /usr/local/include/bam/
5) export PATH=/PATH-to-samtools-0.1.19/:$PATH

6) tar xvfz tophat-2.0.9.OSX_x86_64.tar
7) cd tophat-2.0.9.OSX_x86_64
8) export PATH=$PATH:$PWD

But when I try ./configure --prefix=/usr/local
I receive the error that:
-bash: ./configure: No such file or directory

When I look in the tophat directory, this error makes sense as there is no ./configure there! Here is what I see there:
$ ls -1 tophat-2.0.9.OSX_x86_64
AUTHORS
COPYING
README
bam2fastx
bam_merge
bed_to_juncs
chr25.tophat
contig_to_chr_coords
fix_map_ordering
gtf_juncs
gtf_to_fasta
juncs_db
long_spanning_reads
map2gtf
prep_reads
sam_juncs
segment_juncs
sra_to_solid
tophat
tophat-fusion-post
tophat2
tophat_reports

I greatly appreciate if you could help me with this problem!

Thanks!

[GenoMax]

You downloaded the pre-compiled binary for TopHat from this link?

In this case you do not need to configure/compile anything. You are ready to start using tophat right away from this point on: http://tophat.cbcb.umd.edu/tutorial.shtml#ref

If you are using a standard genome available from iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html) then you can even skip the genome indexing prep part and start mapping your reads: http://tophat.cbcb.umd.edu/tutorial.shtml#toph

[norafar]

Thanks a lot! I realized that I had in fact downloaded the pre-compiled version!