Dear Forum,
I have tried to install tophat on a new mac machine, and although both bowtie and tophat seem to be installed just fine, it seems tophat has trouble finding bowtie. Here is what I get when I run the test command for tophat:
pc248-23:test_data martinobarenco$ tophat -r 20 test_ref reads_1.fq reads_2.fq
[Wed Sep 22 16:04:37 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Sep 22 16:04:37 2010] Preparing output location ./tophat_out/
[Wed Sep 22 16:04:37 2010] Checking for Bowtie index files
[Wed Sep 22 16:04:37 2010] Checking for reference FASTA file
[Wed Sep 22 16:04:37 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system
bowtie is installed on the system and the path has been set in .bash_profile:
pc248-23:test_data martinobarenco$ bowtie --version
bowtie version 0.12.7
64-bit
Built on Franklin.local
Tue Sep 7 14:27:57 PDT 2010
Compiler: gcc version 4.0.1 (Apple Inc. build 5493)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
I have tried to change the versions of tophat (tophat-1.0.14.OSX_x86_64 and tophat-1.0.13, the latter installed "by hand" and with appropriate changes in the PATH in either case) and I get the same results. It worked fine on a linux machine (with v1.0.11) so it must be problem to OSX (and most likely something I did wrong there). Anyone met the same issue?
Many thanks,
Martino
I have tried to install tophat on a new mac machine, and although both bowtie and tophat seem to be installed just fine, it seems tophat has trouble finding bowtie. Here is what I get when I run the test command for tophat:
pc248-23:test_data martinobarenco$ tophat -r 20 test_ref reads_1.fq reads_2.fq
[Wed Sep 22 16:04:37 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Sep 22 16:04:37 2010] Preparing output location ./tophat_out/
[Wed Sep 22 16:04:37 2010] Checking for Bowtie index files
[Wed Sep 22 16:04:37 2010] Checking for reference FASTA file
[Wed Sep 22 16:04:37 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system
bowtie is installed on the system and the path has been set in .bash_profile:
pc248-23:test_data martinobarenco$ bowtie --version
bowtie version 0.12.7
64-bit
Built on Franklin.local
Tue Sep 7 14:27:57 PDT 2010
Compiler: gcc version 4.0.1 (Apple Inc. build 5493)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
I have tried to change the versions of tophat (tophat-1.0.14.OSX_x86_64 and tophat-1.0.13, the latter installed "by hand" and with appropriate changes in the PATH in either case) and I get the same results. It worked fine on a linux machine (with v1.0.11) so it must be problem to OSX (and most likely something I did wrong there). Anyone met the same issue?
Many thanks,
Martino
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