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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