Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add parallelization and additional user options #24

Merged
merged 21 commits into from
Feb 12, 2018
Merged

Add parallelization and additional user options #24

merged 21 commits into from
Feb 12, 2018

Commits on Feb 6, 2018

  1. pass through n_cpus to other scripts

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    6ac2e95 View commit details
    Browse the repository at this point in the history

  2. fix

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    ec60db8 View commit details
    Browse the repository at this point in the history

  3. fix2

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    595d24a View commit details
    Browse the repository at this point in the history

  4. Added parallelization of muscle + hmmbuild steps

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    f855d6d View commit details
    Browse the repository at this point in the history

  5. Add --data-dir to wrapper script usage

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    ae9db20 View commit details
    Browse the repository at this point in the history

  6. format wrapper

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    a1a03d7 View commit details
    Browse the repository at this point in the history

  7. Add conda instructions to README

    @brymerr921
    brymerr921 committed Feb 6, 2018
    Configuration menu
    Copy the full SHA
    af687b3 View commit details
    Browse the repository at this point in the history

Commits on Feb 7, 2018

  1. fix

    @brymerr921
    brymerr921 committed Feb 7, 2018
    Configuration menu
    Copy the full SHA
    15460e9 View commit details
    Browse the repository at this point in the history

  2. Parallelized Step_3!

    @brymerr921
    brymerr921 committed Feb 7, 2018
    Configuration menu
    Copy the full SHA
    27e8114 View commit details
    Browse the repository at this point in the history

  3. Parallelized step 3!!!

    @brymerr921
    brymerr921 committed Feb 7, 2018
    Configuration menu
    Copy the full SHA
    f8ceafb View commit details
    Browse the repository at this point in the history

  4. change default cpus to 4 in wrapper

    @brymerr921
    brymerr921 committed Feb 7, 2018
    Configuration menu
    Copy the full SHA
    71f76e2 View commit details
    Browse the repository at this point in the history

  5. fix parallel on step_0 and step_first

    @brymerr921
    brymerr921 committed Feb 7, 2018
    Configuration menu
    Copy the full SHA
    5822d89 View commit details
    Browse the repository at this point in the history

Commits on Feb 8, 2018

  1. update cpanfile

    @brymerr921
    brymerr921 committed Feb 8, 2018
    Configuration menu
    Copy the full SHA
    5c6787b View commit details
    Browse the repository at this point in the history

  2. Update README.md

    @brymerr921
    brymerr921 committed Feb 8, 2018
    Configuration menu
    Copy the full SHA
    0acf0a8 View commit details
    Browse the repository at this point in the history

  3. fix Step_3 argv issue

    @brymerr921
    brymerr921 committed Feb 8, 2018
    Configuration menu
    Copy the full SHA
    bd1f42d View commit details
    Browse the repository at this point in the history

Commits on Feb 9, 2018

  1. Added option to use diamond instead of blastp

    @brymerr921
    brymerr921 committed Feb 9, 2018
    Configuration menu
    Copy the full SHA
    1bf9de1 View commit details
    Browse the repository at this point in the history

  2. Add option to keep databases

    @brymerr921
    brymerr921 committed Feb 9, 2018
    Configuration menu
    Copy the full SHA
    702fb27 View commit details
    Browse the repository at this point in the history

  3. Improve Step_3 and C script so no more file writes, these modifications 

    were suggested by Simon Roux.
    @brymerr921
    brymerr921 committed Feb 9, 2018
    Configuration menu
    Copy the full SHA
    c5669e9 View commit details
    Browse the repository at this point in the history

  4. Fix sliding and step3

    @brymerr921
    brymerr921 committed Feb 9, 2018
    Configuration menu
    Copy the full SHA
    4c96738 View commit details
    Browse the repository at this point in the history

  5. Use printf in Step_3 instead of echo

    @brymerr921
    brymerr921 committed Feb 9, 2018
    Configuration menu
    Copy the full SHA
    1fbe577 View commit details
    Browse the repository at this point in the history

Commits on Feb 12, 2018

  1. Link to anvio import instructions

    @brymerr921
    brymerr921 committed Feb 12, 2018
    Configuration menu
    Copy the full SHA
    2da3c8f View commit details
    Browse the repository at this point in the history