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