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buske / silva

SilVA: Silent Variant Analysis using random forests
GNU General Public License v3.0
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Error in downloading and unpacking unafold-3.8.tar.gz #6

Open hafizmtalha opened 5 years ago

hafizmtalha commented 5 years ago

I m trying to install silve, and this tool tries to download and unpack unafold-3.8.tar.gz. But the links it is using seems to be not available anymore. Kindly provide the alternative link.

buske commented 5 years ago

Dear @hafizmtalha, unfortunately, the owners of UNAfold have changed the license and stopped distributing it freely. The UNAfold website says you need to obtain the software from ibridge. Unfortunately, there is no other way to download it. To still use SilVA, just use the version without the folding features (which removes the dependency on UNAfold and ViennaRNA): http://compbio.cs.toronto.edu/silva/release/silva-1.1.1-nofolding.tar.gz

hafizmtalha commented 5 years ago

Thanks alot for the help. I found that version while looking for solution on different forums.

On Thu, Dec 20, 2018, 9:26 PM Orion Buske <notifications@github.com wrote:

Dear @hafizmtalha https://github.com/hafizmtalha, the owners of UNAfold have changed the license and stopped distributing it freely. The UNAfold website says you need to obtain the software from ibridge https://www.ibridgenetwork.org/#!/profiles/1045554571442/innovations/1/. Unfortunately, there is no other way to download it. To still use SilVA, just use the version without the folding features (which removes the dependency on UNAfold and ViennaRNA): http://compbio.cs.toronto.edu/silva/release/silva-1.1.1-nofolding.tar.gz

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/buske/silva/issues/6#issuecomment-449055200, or mute the thread https://github.com/notifications/unsubscribe-auth/AkHUK6GgMqLBbirIJKv6e0PaogGZrzc0ks5u67oxgaJpZM4Zbkxa .

rescuz commented 2 months ago

Thanks for your reply. I want to make sure whether the nofolding version of silva-1.1.1 cannot predict the synonymous variants in chrY. Because I met the mention "Removing variants on chromosome Y" in the stdout. The detailed information labeled below: " Found 44535 synonymous variants (1730 dropped) Removing variants on chromosome Y... Left with 0 variants... Annotating with 1000 Genomes Project allele frequency... Loading optimized table from: /data/Project/AI/methods/scripts/pathogenicity/SYN/silva-1.1.1-nofolding/data/1000gp.refGene.pkl Filtering by allele frequency [0, 0.05]... Left with 0 variants... Annotating with mRNA sequence... Loading genes from pickled file: /data/Project/AI/methods/scripts/pathogenicity/SYN/silva-1.1.1-nofolding/data/refGene.pkl Annotating features from MRNA files... Error encountered! "