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.
1 answer
When you download binaries of a program the work of compiling has already been done for you (you do need to get the right binary for your OS). You are now ready to run the program (once you uncompress/unzip the file) without any additional changes.
Try running ./hisat2-build -h from the directory where you have downloaded the program.
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Why not just download the binaries?
Hi. I downloaded the binaries and ran the make on them as well. But cannot get the hisat2 executable.
There's nothing to
make. Just copy the executables to a convenient location and you're done.Hello manu.tiwari!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=208096
This is typically not recommended as it runs the risk of annoying people in both communities.
Hello All
Thank you for all your constructive replies. There was an issue with the downloaded binaries as well as the generated ones. The hisat file was there but as a perl script and somehow the system was not recognizing as an executable. Redownloading the binaries did the trick.
P.S. WouterDecoster- Point noted. Didn"t knew about it. Wouldn"t repeat. And on a lighter note, do the questions really ANNOY? Thank you as well.
That is a standard text. And perhaps 'annoying' is a bit too strong, but it's not nice that 2 communities of volunteers will "work" for you and invest their free time in helping you. One of those communities then spent time for nothing, and that's, well, annoying.
The questions themselves don't, but people answering on one site without seeing that you already received an answer elsewhere is annoying. People are donating their finite time here (and on seqanswers); such behavior tends to result in donated time getting wasted.