Comments (4)
Hi,
I don't have a lot of experience installing on Mac OS. That said, brew in general though should not interfere with the basic functionality of your system. Installing a new compiler with brew should be safe.
Now, any reason why you are installing version 1.1 of Jellyfish, instead of the current version (2.2.5)?
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Hi,
I am working on OS X, too. You are installing a keg-only formula, which means that it will not be symlinked because it could conflict with other versions (brewed or provided by the system) of the same software. Jellyfish-1.1 is keg only, because a newer version is available in homebrew/science. By the way Jellyfish-1.1 is no bottle, only the newer version is bottled (which means precompiled).
I think they kept Jellyfish-1.1 for the installation of the Quake.
You can install a newer version (which is Jellyfish 2.4.x) just with brew install jellyfish
. Being precompiled, the newer Version of Jellyfish does not require the newer version of the compiler at all (except you do not want the precompiled version, because of the SWIG integration).
Cheers
Chris
ps. It is already said, but the installation of the newer GCC with brew does not affect your system.
from jellyfish.
Hi,
can you clarify your statement about the precompiled version and SWIG integration? Is it that the precompiled version does NOT have the SWIG bindings? Or that it does have the SWIG bindings and that somehow creates problems?
from jellyfish.
Hi,
as far as I can tell, the bottled (precompiled) version in brew has no integration of the SWIG bindings. The Jellyfish formula (https://github.com/Homebrew/homebrew-science/blob/master/jellyfish.rb) has not the necessary flags on the configure script as mentioned at Jellyfishs homepage.
Maybe they left the SWIG bindings out, because it is not clear where to integrate them (I think they should be integrated in brews version of perl/python/ruby instead of the ones which are provided by the system).
I am currently compiling Jellyfish from the Master branch of the git repository.
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Related Issues (20)
- Genome masking
- Problem for PacBio Hifi reads in "jellyfish count" command
- Potential error in documentation HOT 1
- How does Jellyfish behave in presence of ambiguous nucleotides (such as N)? HOT 3
- Add Jellyfish to Nix package repository
- standalone C++ API for lock-free concurrent hashmap? HOT 2
- Implementing to count ambiguous bases
- Gzipped fastq files HOT 1
- strange error with query HOT 3
- build failure with gcc-12 HOT 2
- tests/swig_perl flaky - possibly hardware dependent
- Performance regression in Jellyfish 2.3.0
- Is there any way to count kmer and get histo on multi-hosts?
- How to get the version of jellyfish HOT 1
- Package to read in binary .jf output file in python? HOT 2
- Where can I find the 2.0 version of Jellyfish?
- Dramatic output difference between version 2.2.10 and 2.3.0
- out of memory? HOT 1
- kitsune and jellyfish error "Bloom filter file is truncated" HOT 1
- mer_dna.hpp: line 84 HOT 1
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