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Releases: faircloth-lab/phyluce

phyluce v1.7.3

18 Jul 20:29
@brantfaircloth brantfaircloth
v1.7.3
1b361df
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phyluce v1.7.3 Latest
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phyluce is available in several forms. See documentation for additional details. The preferred installation uses conda. phyluce is also available as a Docker container. Both options include all of the dependencies required by phyluce (which are numerous).

Installation

Conda

  1. Install Miniconda by following these instructions
  2. Then, for your operating system:

  • MacOS - M-Series CPU

    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.3/distrib/phyluce-1.7.3-py36-macOS-conda.yml

# the next line must be run at the same time (e.g. do not split it up) - this sets up an x86 environment
CONDA_SUBDIR=osx-64 conda create -n phyluce-1.7.3-x86 python=3.6
conda activate phyluce-1.7.3-x86
conda config --env --set subdir osx-64
# finally, install from the yml file
conda env update --name phyluce-1.7.3-x86 --file phyluce-1.7.3-py36-macOS-conda.yml --prune
# if you are finished
conda deactivate

  • MacOS - Intel CPU

    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.3/distrib/phyluce-1.7.3-py36-macOS-conda.yml
conda env create -n phyluce-1.7.3 --file phyluce-1.7.3-py36-macOS-conda.yml

  • Linux

    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.3/distrib/phyluce-1.7.3-py36-Linux-conda.yml
conda env create -n phyluce-1.7.3 --file phyluce-1.7.3-py36-Linux-conda.yml
  1. Activate and use the environment:
conda activate phyluce-1.7.3 # or phyluce-1.7.3-x86 if using M-series CPU

Docker

  1. Pull the image from Docker Hub:
docker pull fairclothlab/phyluce:1.7.3
  1. See documentation for more specific details, but generally:
docker run fairclothlab/phyluce:1.7.3 <name_of_phyluce_program>

Changes

Bug Fixes

  • fixed an issue concatenating phylip files (closes #307)
  • updated a failing test (that resulted from changes in the BOLD database)
Assets 2

phyluce 1.7.2

27 Jan 15:55
@brantfaircloth brantfaircloth
v1.7.2
171f8ea
This commit was signed with the committer’s verified signature.
brantfaircloth Brant Faircloth
GPG key ID: F76D21AED1F4FFEA
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phyluce 1.7.2

phyluce is available in several forms. See documentation for additional details. The preferred installation uses conda. phyluce is also available as a Docker container. Both options include all of the dependencies required by phyluce (which are numerous).

Installation

Conda

  1. Install Miniconda by following these instructions
  2. Then, for your operating system:

  • MacOS - M-Series CPU

    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.2/distrib/phyluce-1.7.2-py36-macOS-conda.yml

# the next line must be run at the same time (e.g. do not split it up) - this sets up an x86 environment
CONDA_SUBDIR=osx-64 conda create -n phyluce-1.7.2-x86 python=3.6
conda activate phyluce-1.7.2-x86
conda config --env --set subdir osx-64
# finally, install from the yml file
conda env update --name phyluce-1.7.2-x86 --file phyluce-1.7.2-py36-macOS-conda.yml --prune
# if you are finished
conda deactivate

  • MacOS - Intel CPU

    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.2/distrib/phyluce-1.7.2-py36-macOS-conda.yml
conda env create -n phyluce-1.7.2 --file phyluce-1.7.2-py36-macOS-conda.yml

  • Linux

    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.2/distrib/phyluce-1.7.2-py36-Linux-conda.yml
conda env create -n phyluce-1.7.2 --file phyluce-1.7.2-py36-Linux-conda.yml
  1. Activate and use the environment:
conda activate phyluce-1.7.1 # or phyluce-1.7.2-x86 if using M-series CPU

Docker

  1. Pull the image from Docker Hub:
docker pull fairclothlab/phyluce:1.7.2
  1. See documentation for more specific details, but generally:
docker run fairclothlab/phyluce:1.7.2 <name_of_phyluce_program>

Changes

Bug Fixes

  • fixed a dependency issue (closes #290)
  • added M1 installation procedure (closes #281)
  • updated testing scripts (to use 20.04)
  • updated docker build ( to use bash in place of sh)
Assets 2

phyluce 1.7.1

12 Mar 21:19
@brantfaircloth brantfaircloth
v1.7.1
7044ef2
This commit was signed with the committer’s verified signature.
brantfaircloth Brant Faircloth
GPG key ID: F76D21AED1F4FFEA
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phyluce 1.7.1

phyluce is available in several forms. See documentation for additional details. The preferred installation uses conda. phyluce is also available as a Docker container. Both options include all of the dependencies required by phyluce (which are numerous).

Installation

Conda

  1. Install Miniconda by following these instructions
  2. Then, for your operating system:
  • MacOS 
    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.1/distrib/phyluce-1.7.1-py36-macOS-conda.yml
conda env create -n phyluce-1.7.1 --file phyluce-1.7.1-py36-macOS-conda.yml
  • Linux 
    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.1/distrib/phyluce-1.7.1-py36-Linux-conda.yml
conda env create -n phyluce-1.7.1 --file phyluce-1.7.1-py36-Linux-conda.yml
  1. Activate and use the environment:
conda activate phyluce-1.7.1

Docker

  1. Pull the image from Docker Hub:
docker pull fairclothlab/phyluce:1.7.1
  1. See documentation for more specific details, but generally:
docker run fairclothlab/phyluce:1.7.1 <name_of_phyluce_program>

Changes

Bug Fixes

  • fix an issue with feedback regarding removal of existing directories/files
  • fix an issue with slicing fasta sequences from genomes (using twobit files)

Maintenance

  • small formatting fix in documentation for harvesting UCEs
Assets 2

phyluce v1.7.0

04 Mar 18:24
@brantfaircloth brantfaircloth
v1.7.0
27cc404
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phyluce v1.7.0

phyluce is available in several forms. See documentation for additional details. The preferred installation uses conda. phyluce is also available as a Docker container. Both options include all of the dependencies required by phyluce (which are numerous).

Installation

Conda

  1. Install Miniconda by following these instructions
  2. Then, for your operating system:
  • MacOS 
    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.0/distrib/phyluce-1.7.0-py36-macOS-conda.yml
conda env create -n phyluce-1.7.0 --file phyluce-1.7.0-py36-macOS-conda.yml
  • Linux 
    wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.0/distrib/phyluce-1.7.0-py36-Linux-conda.yml
conda env create -n phyluce-1.7.0 --file phyluce-1.7.0-py36-Linux-conda.yml
  1. Activate and use the environment:
conda activate phyluce-1.7.0

Docker

  1. Pull the image from Docker Hub:
docker pull fairclothlab/phyluce:1.7.0
  1. See documentation for more specific details, but generally:
docker run fairclothlab/phyluce:1.7.0 <name_of_phyluce_program>

Changes

Features

  • add unit tests for all critical operations and some non-critical operations
  • add "workflows" for complex, multi-step jobs (replaces older code for phasing and coverage computation)
  • add code to cleanup spades assemblies

Bug Fixes

  • test for common error which would cause sqlite table formation to fail
  • change RAM parameters for Spades runs (now a command-line option)

Maintenance

  • update all code to work with python3.6 - no more python2 support
  • update installation/build mechanisms for github actions
  • update logs with some color for different events
  • change notices to users for incompatible operations per operating system
  • documentation re-organized and updated
  • use smaller data sets in documentation examples
  • update documentation

Major Removals

  • trinity has been removed - recommend using spades
  • the code for computing (trinity) coverage has been removed (see new workflow)
  • the old phasing code has been removed (see new phasing workflow)
  • all code formerly in ATTIC has been removed
  • most code for inferring gene trees has been removed (there are better options and this was mostly out-of-scope of phyluce)
Assets 2