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Old 06-03-2017, 03:34 AM   #1
Dros
Junior Member
 
Location: Germany

Join Date: Jun 2017
Posts: 1
Default HISAT2 executable

Hi

I am trying to use HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml) to do alignments and downstram processing.
The problem that I encounter is that I am not able to get a hisat executable file after running the
Code:
make
command (I am on Ubuntu 16.04).
Running
Code:
make
on the downloaded binary (or the source) file gives me all the other required executables (hisat2-align-s, hisat2-align-l, hisat2-build, hisat2-build-s, hisat2-build-l, hisat2-inspect, hisat2-inspect-s and hisat2-inspect-l) but not hisat2 which is required in the alignment step.
May be I am just missing some small point here but any help will be great.

Thanks.
Dros
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Old 06-03-2017, 10:46 AM   #2
mastal
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Location: uk

Join Date: Mar 2009
Posts: 667
Default

You don't need to run 'make' if you download the binary, only if you are trying to build from the source code.

What version of HISAT2 are you using?

I just downloaded the Linux binary for version 2.0.5, unzipped the file, and hisat2 is present, along with the other hisat2 programs.

Last edited by mastal; 06-03-2017 at 10:56 AM.
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