Looks like the "development" package for zlib is missing. Rather than building SAMtools from source, you may want to check if there is a packaged version for your Linux distribution. The package manager [apt-get on Ubuntu(?); I'm on CentOS and use yum] should handle bringing in any dependencies if they are not already installed. If you do indeed want to build from source, use your package manager to install the needed dependency, typically something like zlib-devel. -- Olen On Mon, Aug 1, 2011 at 13:53, Luciano Cosme <cosme.simple@gmail.com> wrote:

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. 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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