> Hi Everyone,
>    I am running galaxy locally (ubuntu 11.04) and I am having problem with
> samtools. When I am running TopHat I get an error message saying that could
> not locate samtools. Of course I did everything described in
> http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
>  Here is the error message:
>
> Error in tophat:
>
> [Mon Aug  1 13:03:53 2011] Beginning TopHat run (v1.3.1)
> -----------------------------------------------
> [Mon Aug  1 13:03:53 2011] Preparing output location ./tophat_out/
> [Mon Aug  1 13:03:53 2011] Checking for Bowtie index files
> [Mon Aug  1 13:03:53 2011] Checking for reference FASTA file
>       Warning: Could not find FASTA file /tmp/tmpkcZN3L/dataset_26.dat.fa
> [Mon Aug  1 13:03:53 2011] Reconstituting reference FASTA file from Bowtie 
> index
> Executing: /bin/bowtie-inspect /tmp/tmpkcZN3L/dataset_26.dat > 
> ./tophat_out/tmp/dataset_26.dat.fa
> [Mon Aug  1 13:04:41 2011] Checking for Bowtie
>       Bowtie version:                  0.12.7.0
> [Mon Aug  1 13:04:42 2011] Checking for Samtools
> Error locating program: samtools
>
>
> When I run "make" in the samtools directory I also get an error message:
>
> koala2@aedes:~/Desktop/galaxy/samtools$ make
> make[1]: Entering directory `/home/koala2/Desktop/galaxy/samtools'
> make[2]: Entering directory `/home/koala2/Desktop/galaxy/samtools'
> gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
> -I. bgzf.c -o bgzf.o
> In file included from bgzf.c:36:0:
> bgzf.h:30:18: fatal error: zlib.h: No such file or directory
> compilation terminated.
>

Hi,

>From the above lines error message it is clear that zlib.h is not installed
in your machine,
On ubuntu try to install zlib1g-dev package via apt-get install,

HTH, Vipin



> make[2]: *** [bgzf.o] Error 1
> make[2]: Leaving directory `/home/koala2/Desktop/galaxy/samtools'
> make[1]: *** [lib-recur] Error 1
> make[1]: Leaving directory `/home/koala2/Desktop/galaxy/samtools'
> make: *** [all-recur] Error 1
>
> I also followed the installation guide from samtools, but did not work
> either.
>
> Unfortunately I found myself spending more time installing tools than using
> it. Yes I am a newbie.
> Thank you.
>
> Luciano
>
>
>
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