Hi there,
This is quite vexing, Bowtie2 is in my path but Tophat complains that it is not on the system.
I am using Amazon Linux, 64-bit and I installed binaries of Tophat, Bowtie and cufflinks. Samtools was compiled from source code.
.bash_profile has the following:
TUX_PATH=/home/ec2-user/software
PATH=$PATH:$TUX_PATH/bowtie:$TUX_PATH/cufflinks:$TUX_PATH/tophat:$TUX_PATH/samtools
export PATH
Typing "bowtie2 --version" from any subdirectory yields:
/home/ec2-user/software/bowtie/bowtie2-align-s version 2.2.1
64-bit
Built on igm2
Likewise, Tophat, Cufflinks and Samtools are all found from any subdirectory.
However, running TopHat using a script that works fine on my own Linux box at home yields:
Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
I'm at my wits end here.
Thanks,
Dr Funkenstein
This is quite vexing, Bowtie2 is in my path but Tophat complains that it is not on the system.
I am using Amazon Linux, 64-bit and I installed binaries of Tophat, Bowtie and cufflinks. Samtools was compiled from source code.
.bash_profile has the following:
TUX_PATH=/home/ec2-user/software
PATH=$PATH:$TUX_PATH/bowtie:$TUX_PATH/cufflinks:$TUX_PATH/tophat:$TUX_PATH/samtools
export PATH
Typing "bowtie2 --version" from any subdirectory yields:
/home/ec2-user/software/bowtie/bowtie2-align-s version 2.2.1
64-bit
Built on igm2
Likewise, Tophat, Cufflinks and Samtools are all found from any subdirectory.
However, running TopHat using a script that works fine on my own Linux box at home yields:
Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
I'm at my wits end here.
Thanks,
Dr Funkenstein
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