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Recent Releases of phyluce

phyluce - phyluce v1.7.3

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 ```bash 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 bash 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 bash 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: bash 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: bash docker pull fairclothlab/phyluce:1.7.3
  2. See documentation for more specific details, but generally: bash 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)

- Python
Published by brantfaircloth over 2 years ago

phyluce - 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 ```bash 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 bash 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 bash 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: bash 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: bash docker pull fairclothlab/phyluce:1.7.2
  2. See documentation for more specific details, but generally: bash 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)

- Python
Published by brantfaircloth about 3 years ago

phyluce - 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 bash 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 bash 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
  3. Activate and use the environment: bash conda activate phyluce-1.7.1

Docker

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

- Python
Published by brantfaircloth about 5 years ago

phyluce - 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 bash 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 bash 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
  3. Activate and use the environment: bash conda activate phyluce-1.7.0

Docker

  1. Pull the image from Docker Hub: bash docker pull fairclothlab/phyluce:1.7.0
  2. See documentation for more specific details, but generally: bash 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)

- Python
Published by brantfaircloth about 5 years ago