SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Samtools "is recognized as '*'" "truncated file" error axiom7 Bioinformatics 3 11-26-2014 03:53 AM
TopHat "configure: No such file or directory" norafar Introductions 2 07-01-2013 08:44 AM
TopHat "-M" option and Unmapped.bam file washy RNA Sequencing 2 05-24-2013 07:20 AM
pileup file symbols "<" and ">" geraldgsw Bioinformatics 3 12-30-2011 09:19 AM
The position file formats ".clocs" and "_pos.txt"? Ist there any difference? elgor Illumina/Solexa 0 06-27-2011 08:55 AM

Reply
 
Thread Tools
Old 06-28-2013, 07:12 PM   #1
norafar
Junior Member
 
Location: New York, USA

Join Date: May 2013
Posts: 5
Default TopHat "configure: No such file or directory"

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!
norafar is offline   Reply With Quote
Old 06-28-2013, 07:54 PM   #2
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,155
Default

You have downloaded the precompiled, binary distribution of tophat for OSX. There is no need to run configure and make here, the software is already built and ready to run.
kmcarr is offline   Reply With Quote
Reply

Tags
conf error, configuration, tophat, tophat installation

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:34 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO