I'd like to install HISAT2 on Mac OS X El Capitan. I have installed Xcode and gcc in my system.I downloaded the source file and unzipped it (hisat2-2.0.0-beta). I have tried running gmake hisat2-2.0.0-beta (case 1) and using the -h command line (case two) and Im getting the following output (below). Please advise.
Case 1:
Nishas-MacBook-Pro:hisat2-2.0.0-beta Nisha$ make hisat2
Agreeing to the Xcode/iOS license requires admin privileges, please re-run as root via sudo.
Nishas-MacBook-Pro:hisat2-2.0.0-beta Nisha$
Case 2:
Nishas-MacBook-Pro:hisat2-2.0.0-beta Nisha$ ./hisat2 -h
(ERR): Expected hisat to be in same directory with hisat-align:
/Users/Nisha/Desktop/hisat2-2.0.0-beta/
Exiting now ...
Nishas-MacBook-Pro:hisat2-2.0.0-beta Nisha$
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2 answers
There is generally (for most standard software in bioinformatics) o need to compile from source. Either get pre-compiled binaries provided by the developers as Sej Modha suggests or install via a package manager such as anaconda. This will save you both time and effort.
Please be sure to use google and the search function for upcoming problems as you seem to get started in the field. Most standard problems have been encountered, asked and answered before :)
Save yourself a lot of time using conda, or better docker. You'll find how to do it here: https://bioconda.github.io/recipes/hisat2/README.html
In case you don;t have docker or admin permissions on you mac, you can install miniconda: enter link description here
If you finally want to save even more time (and make your analyses more easily reproducible), use Docker together with nextflow: enter link description here
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You could download the pre-built binaries for MacOS instead of building the tool from source - http://ccb.jhu.edu/software/hisat2/dl/hisat2-2.1.0-OSX_x86_64.zip