Cannot access markers.tgz from http://edhar.genomecenter.ucdavis.edu/~koadman

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csi...@lbl.gov

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Jan 5, 2018, 4:19:43 PM1/5/18
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PhyloSift fails because it cannot download the marker DB file from: http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz
Can you please provide an alternative location for markers.tgz?

Similarly, the "easy way" of installing PhyloSift does not work as http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/releases/phylosift_v1.0.1.tar.bz2 cannot be downloaded.


$ phylosift all my_seq.fasta

PhyloSift -- Phylogenetic analysis of genomes and metagenomes
(c) 2011, 2012 Aaron Darling and Guillaume Jospin

CITATION:
PhyloSift. A. E. Darling, G. Jospin, E. Lowe, F. A. Matsen, H. M. Bik, J. A. Eisen. Submitted to PeerJ


PhyloSift incorporates several other software packages, please consider also citing the following papers:


pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
Frederick A Matsen, Robin B Kodner, and E Virginia Armbrust
BMC Bioinformatics 2010, 11:538

Adaptive seeds tame genomic sequence comparison.
SM Kielbasa, R Wan, K Sato, P Horton, MC Frith
Genome Research 2011.

Infernal 1.0: Inference of RNA alignments
E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy
Bioinformatics 25:1335-1337 (2009)

  Bowtie: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
  Langmead B, Trapnell C, Pop M, Salzberg SL. Genome Biol 10:R25.

  HMMER 3.0 (March 2010); http://hmmer.org/
  Copyright (C) 2010 Howard Hughes Medical Institute.
  Freely distributed under the GNU General Public License (GPLv3).

  Phylogenetic Diversity within Seconds.
Bui Quang Minh, Steffen Klaere and Arndt von Haeseler
Syst Biol (2006) 55 (5): 769-773.
Attempting to get exclusive rights to the marker DB. Possibly waiting for another PhyloSift to release the file lock
Marker version unknown, downloading markers
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (6) Could not resolve host: edhar.genomecenter.ucdavis.edu
tar: Error opening archive: Failed to open 'markers.tgz'


Guillaume Jospin

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Jan 5, 2018, 5:43:40 PM1/5/18
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Yes that server died recently. 
We set up an alternative download location but you will need to download the markers manually. 



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csi...@lbl.gov

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Jan 8, 2018, 8:39:25 PM1/8/18
to PhyloSift
Thanks for your quick reply!
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