Comments (4)
Hi Cristian,
I think you need to set up the gcc in a proper way:
http://www.ficksworkshop.com/blog/post/installing-gcc-on-mac
and then this should work out of the build directory. Please delete and create the directory again.
cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 ..
Cheers
Fritz
from sniffles.
It might be also easy to check out bioconda for installing:
https://bioconda.github.io/recipes/sniffles/README.html
Cheers
Fritz
from sniffles.
Hi Fritz,
Thank you for answering my questions. I tried installing gcc with macports and then use the cmake command but that did not work. I tried 'conda install sniffles' but that also failed. But then, taking inspiration from my NGM-LR installation, I used 'conda install --channel https://conda.anaconda.org/bioconda sniffles' and it seems to have worked.
Best wishes,
Cristian.
from sniffles.
Hi Cristian,
awesome that it worked.
Thanks
Fritz
from sniffles.
Related Issues (20)
- Sniffles2 Error: Malformed CIGAR HOT 1
- Why are there fewer SVs with --mosaic? HOT 1
- Can Sniffles2 detect SV variants which have no spanning reads covering the whole variant? HOT 11
- How to make sniffles do a better job in splitting insertions at the same location into two het calls? HOT 1
- Multisample VCF seems to only report final .snf processed HOT 3
- support needed: if ALT is base-level identical across samples from a muli-sample vcf generated by sniffles2? HOT 7
- Force Calling Errors HOT 2
- Feature Request - Force calling FORMAT header lines HOT 3
- how sniffles reflect Cell heterogeneity HOT 3
- How to view tandem repeats in the VCF? HOT 1
- How to view the tandem repeats in the VCF file generated by Sniffles2? HOT 5
- [Question] SNF compatibility across version HOT 1
- sniffles 2.3 is not in bioconda yet? HOT 3
- Overcalling BNDs? HOT 1
- Sniffle2.3 installation issue HOT 4
- v2.3.2 error HOT 5
- Sniffles v2.3.2 never exits HOT 11
- vcf_out may be unbound in sniffles v2.3.2 HOT 2
- Phased SV calling HOT 4
- Sniffles error HOT 13
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from sniffles.