niemasd/FAVITES

Issues

• Error on running run_favites.py

  #44 opened 8 months ago by MarriaK
  4

• ERROR?

  #43 opened a year ago by liamxg
  2

• config_designer.py fails to write JSON

  #42 opened 2 years ago by ArtPoon
  2

• Sampling times file not found

  #41 opened 3 years ago by pekarj
  3

• run_favites_docker.py only works on Linux with sudo

  #40 opened 3 years ago by ghart-IDM
  3

• Add SANTA-SIM

  #39 opened 4 years ago by niemasd
  0

• Enquiry about backward-in-time models

  #38 opened 4 years ago by Hc1023
  5

• Add ReSeq

  #37 opened 4 years ago by niemasd
  0

• Allow user to specify sample times in file

  #36 opened 4 years ago by niemasd
  1

• Issue with label_internal_nodes helper script

  #35 opened 4 years ago by pekarj
  1

• Does not properly identify seed nodes

  #34 opened 4 years ago by pekarj
  2

• "KeyError: 'None'", for my Transmission Network File

  #30 opened 5 years ago by pekarj
  2

• Create Google Group or something where we only announce input/output changes

  #14 opened 5 years ago by niemasd
  1

• Create transmission module implementations for EoN

  #33 opened 5 years ago by niemasd
  0

• No such file or directory: 'ID_xxx_simple.nex'

  #32 opened 5 years ago by yueyujiang
  2

• Running config_designer.py causes my computer account logging out

  #31 opened 5 years ago by yueyujiang
  3

• Breaks when using "-u" in command line and not specifying the version

  #29 opened 5 years ago by pekarj
  2

• Implement πBUSS as a SequenceEvolution module

  #28 opened 5 years ago by niemasd
  0

• float('inf') in CONFIG file doesn't work in run_favites_docker.py (and potentially Singularity)

  #27 opened 6 years ago by niemasd
  1

• Create helper script that labels internal nodes of output trees

  #26 opened 6 years ago by niemasd
  1

• Allow some communities to have 0 seeds

  #25 opened 6 years ago by niemasd
  1

• Singularity Compatible Version of Favites Issue

  #24 opened 6 years ago by sinamlk
  3

• Seed trees may need root branches added

  #23 opened 6 years ago by niemasd
  1

• Don't start all HIV seeds in AU (HIV Granich)

  #16 opened 7 years ago by niemasd
  1

• Create Bash script (like Dockerfile) to automate installing all dependencies

  #20 opened 7 years ago by niemasd
  1

• Create script to run Docker via Singularity

  #22 opened 7 years ago by niemasd
  5

• Implement EpiModel plugins for FAVITES

  #21 opened 7 years ago by niemasd
  1

• Starting at later steps of workflow

  #17 opened 7 years ago by niemasd
  7

• example config file now working

  #18 opened 7 years ago by smirarab
  1

• Example files output directory

  #19 opened 7 years ago by smirarab
  1

• Check (and potentially reimplement) reading transmission network from file

  #9 opened 7 years ago by niemasd
  1

• Modules that load from user-specified file don't work in Docker

  #10 opened 7 years ago by niemasd
  1

• In run_favites_docker.py, only call URLLib if necessary

  #13 opened 7 years ago by niemasd
  1

• AssertionError in run_favites.py manually

  #15 opened 7 years ago by smazrouee
  2

• zipped trees seem to have issues (under error_free_files/phylogenetic_trees)

  #12 opened 7 years ago by smazrouee
  9

• Parameter 'vts_max_attempts' not found in config

  #11 opened 7 years ago by smazrouee
  4

• running error on local machibe

  #5 opened 7 years ago by smazrouee
  11

• Kill VirusTreeSimulator after x number of failures to coalesce

  #7 opened 7 years ago by niemasd
  4

• PANGEA doesn't work in Docker image

  #8 opened 7 years ago by niemasd
  1

• Automated DockerHub repository tests

  #2 opened 7 years ago by niemasd
  2

• running error on Calab

  #6 opened 7 years ago by smazrouee
  4

• Add random number generator seed functionality

  #3 opened 7 years ago by niemasd
  1

• No seq file generated

  #4 opened 7 years ago by smazrouee
  8

• Deprecated DendroPy function usage

  #1 opened 7 years ago by niemasd
  2