so I work in an institution where the CCS dept is responsible for installation.
When trying to run TopHat, I get this output:
[Wed May 26 20:18:38 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Wed May 26 20:18:38 2010] Preparing output location ./tophat_out/
[Wed May 26 20:18:38 2010] Checking for Bowtie index files
[Wed May 26 20:18:38 2010] Checking for reference FASTA file
[Wed May 26 20:18:38 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system
the way they installed tophat and bowtie is the following:
../a/b.directory_c/tophat/1.0.13/bin/tophat (stuff)
../a/b/directory_c/bowtie/0.12.5/bowtie (stuff)
while I wouldn't mind moving stuff around to figure out how to get things to work, having them do it is painful (and time consuming). Can someone tell me how they ought to be orientated to run top hat properly
When trying to run TopHat, I get this output:
[Wed May 26 20:18:38 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Wed May 26 20:18:38 2010] Preparing output location ./tophat_out/
[Wed May 26 20:18:38 2010] Checking for Bowtie index files
[Wed May 26 20:18:38 2010] Checking for reference FASTA file
[Wed May 26 20:18:38 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system
the way they installed tophat and bowtie is the following:
../a/b.directory_c/tophat/1.0.13/bin/tophat (stuff)
../a/b/directory_c/bowtie/0.12.5/bowtie (stuff)
while I wouldn't mind moving stuff around to figure out how to get things to work, having them do it is painful (and time consuming). Can someone tell me how they ought to be orientated to run top hat properly
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