IMP: vscode-specific project structuring (#6)
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26 changed files with 1161 additions and 982 deletions
109
.gitignore
vendored
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109
.gitignore
vendored
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@ -0,0 +1,109 @@
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# Created by https://www.gitignore.io/api/python
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# Edit at https://www.gitignore.io/?templates=python
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### Python ###
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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||||
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# End of https://www.gitignore.io/api/python
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1
.gitmodules
vendored
1
.gitmodules
vendored
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@ -1,3 +1,4 @@
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[submodule "dotbot"]
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path = dotbot
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url = https://github.com/anishathalye/dotbot
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ignore = dirty
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12
README.md
12
README.md
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@ -18,7 +18,6 @@ $ nix-env -i \
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docker \
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git \
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htop \
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mr \
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postgresql \
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reattach-to-user-namespace \
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silver-searcher \
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@ -28,13 +27,18 @@ $ nix-env -i \
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xz
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$ base16_ashes
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$ code --install-extension AndrsDC.base16-themes
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$ code --install-extension ecmel.vscode-html-css
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$ code --install-extension formulahendry.auto-close-tag
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$ code --install-extension hollowtree.vue-snippets
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$ code --install-extension JakeBecker.elixir-ls
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$ code --install-extension karigari.chat
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$ code --install-extension lextudio.restructuredtext
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$ code --install-extension ms-python.python
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$ code --install-extension ms-vscode.Go
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$ code --install-extension ms-vsliveshare.vsliveshare
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$ code --install-extension redhat.vscode-yaml
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$ code --install-extension vscodevim.vim
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$ code --install-extension alefragnani.project-manager
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$ code --install-extension donjayamanne.githistory
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$ code --install-extension wakatime.vscode-wakatime
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$ mr checkout
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$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
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$ sudo sh Miniconda3-latest-MacOSX-x86_64.sh -p /opt/miniconda3 -b
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$ sudo conda update conda
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54
bin/bootstrap_git_repos.py
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54
bin/bootstrap_git_repos.py
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@ -0,0 +1,54 @@
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import json
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import os
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import subprocess
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from qiime2_projects import PROJECTS as Q2_PROJECTS
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from mds_projects import PROJECTS as MDS_PROJECTS
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from personal_projects import PROJECTS as PERSONAL_PROJECTS
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def fetch_projects(projects, base_fp, remotes):
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for org, repos in projects.items():
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base_fp = os.path.join('~', 'projects', base_fp)
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base_fp = os.path.expanduser(base_fp)
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for repo in repos:
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print('repo: %s/%s' % (org, repo))
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repo_fp = os.path.join(base_fp, repo)
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repo_fp = os.path.expanduser(repo_fp)
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if not os.path.isdir(repo_fp):
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url = 'https://github.com/%s/%s' % (org, repo)
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subprocess.run(['git', 'clone', url, repo_fp])
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subprocess.run(['git', 'remote', 'rename', 'origin', org],
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cwd=repo_fp)
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for remote in remotes:
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url = 'https://github.com/%s/%s' % (remote, repo)
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try:
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subprocess.run(['git', 'remote', 'add', remote, url],
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cwd=repo_fp, check=True,
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capture_output=True)
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except subprocess.CalledProcessError as e:
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msg = 'remote %s already exists' % (remote, )
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if msg not in str(e.stderr):
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raise
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try:
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subprocess.run(['git', 'fetch', remote],
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cwd=repo_fp, check=True,
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capture_output=True)
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except subprocess.CalledProcessError as e:
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if url not in str(e.stderr):
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raise
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else:
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subprocess.run(['git', 'remote', 'remove', remote],
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cwd=repo_fp)
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if __name__ == '__main__':
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remotes = ['thermokarst', 'ebolyen', 'gregcaporaso', 'ChrisKeefe',
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'Oddant1', 'nbokulich', 'andrewsanchez', 'David-Rod']
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fetch_projects(Q2_PROJECTS, 'qiime2', remotes)
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fetch_projects(MDS_PROJECTS, 'mds', [])
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fetch_projects(PERSONAL_PROJECTS, 'personal', [])
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57
bin/generate_vscode_workspaces.py
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57
bin/generate_vscode_workspaces.py
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@ -0,0 +1,57 @@
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import json
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import os
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from qiime2_projects import PROJECTS as Q2_PROJECTS
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from mds_projects import PROJECTS as MDS_PROJECTS
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from personal_projects import PROJECTS as PERSONAL_PROJECTS
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def render_vscode_workspace(projects, project_name, output_fp,
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include_dotfiles=True, extra_dirs=None):
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folders = []
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for org, repos in projects.items():
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for repo in repos:
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fp = os.path.join('~', 'projects', project_name, repo)
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fp = os.path.expanduser(fp)
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folders.append({'name': repo.lower(),
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'path': fp})
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if include_dotfiles:
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dotfile_fp = os.path.join(os.sep, 'Users', 'matthew', '.dotfiles')
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folders.append({'name': 'dotfiles',
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'path': dotfile_fp})
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if extra_dirs is not None:
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for name, path in extra_dirs.items():
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fp = os.path.join('~', 'projects', project_name, path)
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fp = os.path.expanduser(fp)
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folders.append({'name': name,
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'path': fp})
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with open(output_fp, 'w') as fh:
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json.dump({'folders': sorted(folders, key=lambda x: x['name'])},
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fh, sort_keys=True, indent=4)
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if __name__ == '__main__':
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def qws(ws_number: int):
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return render_vscode_workspace(
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Q2_PROJECTS,
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'qiime2',
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os.path.join('vscode', 'qiime2-%d.code-workspace' % (ws_number, )),
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extra_dirs={'data': 'data'},
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)
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[qws(i) for i in range(1, 4)]
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render_vscode_workspace(
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MDS_PROJECTS,
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'mds',
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os.path.join('vscode', 'mds.code-workspace'),
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)
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render_vscode_workspace(
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PERSONAL_PROJECTS,
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'personal',
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os.path.join('vscode', 'personal.code-workspace'),
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)
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10
bin/mds_projects.py
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10
bin/mds_projects.py
Normal file
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@ -0,0 +1,10 @@
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PROJECTS = {
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'thermokarst': [
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'ccdb-api',
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'ccdb-web',
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'tucotuco',
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'fathm',
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'hibernators',
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'hibernators-web',
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],
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}
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5
bin/personal_projects.py
Normal file
5
bin/personal_projects.py
Normal file
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@ -0,0 +1,5 @@
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PROJECTS = {
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'thermokarst': [
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'elixir-class',
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],
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}
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77
bin/qiime2_projects.py
Normal file
77
bin/qiime2_projects.py
Normal file
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@ -0,0 +1,77 @@
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PROJECTS = {
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'qiime2': [
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'Keemei',
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'action-library-packaging',
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'busywork',
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'data302',
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'dev-docs',
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'discourse-unhandled-tagger',
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'docs',
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'environment-files',
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'library',
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'logos',
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'paper2',
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'q2-alignment',
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'q2-composition',
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'q2-cutadapt',
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'q2-dada2',
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'q2-deblur',
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'q2-demux',
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'q2-diversity',
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'q2-diversity-lib',
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'q2-emperor',
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'q2-feature-classifier',
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'q2-feature-table',
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'q2-fragment-insertion',
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'q2-gneiss',
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'q2-longitudinal',
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'q2-metadata',
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'q2-mystery-stew',
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'q2-phylogenomics',
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'q2-phylogeny',
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'q2-quality-control',
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'q2-quality-filter',
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'q2-sample-classifier',
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'q2-shogun',
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'q2-taxa',
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'q2-types',
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'q2-vsearch',
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'q2cli',
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'q2cwl',
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'q2galaxy',
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'q2studio',
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'q2templates',
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'q2view',
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'qiime2',
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'qiime2.github.io',
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'template-repo',
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'view.qiime2.org',
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'vm-playbooks',
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'workshop-playbooks',
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'workshops.qiime2.org',
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],
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'caporaso-lab': [
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'caporaso-lab.github.io',
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'pretrained-feature-classifiers',
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],
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'gregcaporaso': [
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'caporaso-lab-secrets',
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'qiime2-meta-figures',
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],
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'biocore': [
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'scikit-bio',
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'deblur',
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],
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'thermokarst': [
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'q2-no-op',
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'busywork2_action_playground',
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],
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'bioconda': [
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'bioconda-recipes',
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]
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}
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2
dotbot
2
dotbot
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@ -1 +1 @@
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Subproject commit ef558f85d917c7d2fb52c17db10f0996ef92cb3f
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Subproject commit 5d83f9e797b1950199e127a8196803f5e33e0916
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@ -2,7 +2,7 @@
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name = Matthew Dillon
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email = matthewrdillon@gmail.com
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[core]
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editor = code --wait
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editor = vim
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excludesfile = /Users/matthew/.gitignore_global
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[color]
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diff = auto
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|
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1
install
1
install
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@ -9,6 +9,7 @@ DOTBOT_BIN="bin/dotbot"
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BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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cd "${BASEDIR}"
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git -C "${DOTBOT_DIR}" submodule sync --quiet --recursive
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git submodule update --init --recursive "${DOTBOT_DIR}"
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"${BASEDIR}/${DOTBOT_DIR}/${DOTBOT_BIN}" -d "${BASEDIR}" -c "${CONFIG}" "${@}"
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|
|
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@ -1,17 +1,28 @@
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- clean: ['~']
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- clean:
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- '~'
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- create:
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- ~/projects/qiime2
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- ~/projects/qiime2/data/moving-pictures
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- ~/projects/mds
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- ~/projects/personal
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- shell:
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- python3 bin/generate_vscode_workspaces.py
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- python3 bin/bootstrap_git_repos.py
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|
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- link:
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~/.tmux.conf: tmux.conf
|
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~/.gitconfig: git/gitconfig
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~/.gitignore_global: git/gitignore_global
|
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~/.psqlrc: psqlrc
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~/.zpreztorc: zsh/zpreztorc
|
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~/.zlogin: zsh/zlogin
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~/.zlogout: zsh/zlogout
|
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~/.zprofile: zsh/zprofile
|
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~/.zshenv: zsh/zshenv
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~/.zshrc: zsh/zshrc
|
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~/.mrconfig: mrconfig
|
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~/.tmux.conf: tmux.conf
|
||||
~/.gitconfig: git/gitconfig
|
||||
~/.gitignore_global: git/gitignore_global
|
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~/.npmrc: npmrc
|
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~/.psqlrc: psqlrc
|
||||
~/.zpreztorc: zsh/zpreztorc
|
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~/.zlogin: zsh/zlogin
|
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~/.zlogout: zsh/zlogout
|
||||
~/.zprofile: zsh/zprofile
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~/.zshenv: zsh/zshenv
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~/.zshrc: zsh/zshrc
|
||||
~/Library/Application Support/Code/User/settings.json:
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create: true
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path: vscode/settings.json
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|
|
@ -21,6 +32,8 @@
|
|||
~/Library/Application Support/Code/User/tasks.json:
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create: true
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||||
path: vscode/tasks.json
|
||||
~/Library/Application Support/Code/User/globalStorage/alefragnani.project-manager/projects.json:
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create: true
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path: vscode/projects.json
|
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~/qiime2-1.code-workspace: vscode/qiime2-1.code-workspace
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~/qiime2-2.code-workspace: vscode/qiime2-2.code-workspace
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~/qiime2-3.code-workspace: vscode/qiime2-3.code-workspace
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~/mds.code-workspace: vscode/mds.code-workspace
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~/personal.code-workspace: vscode/personal.code-workspace
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|
|
|
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|
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@ -1,97 +0,0 @@
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import json
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|
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|
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qiime2_projects = [
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'Keemei',
|
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'busywork',
|
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'data.qiime2.org',
|
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'dev-docs',
|
||||
'discourse-unhandled-tagger',
|
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'docs',
|
||||
'environment-files',
|
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'galaxy',
|
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'library',
|
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'logos',
|
||||
'q2-alignment',
|
||||
'q2-composition',
|
||||
'q2-cutadapt',
|
||||
'q2-dada2',
|
||||
'q2-deblur',
|
||||
'q2-demux',
|
||||
'q2-diversity',
|
||||
'q2-diversity-lib',
|
||||
'q2-emperor',
|
||||
'q2-feature-classifier',
|
||||
'q2-feature-table',
|
||||
'q2-fragment-insertion',
|
||||
'q2-gneiss',
|
||||
'q2-longitudinal',
|
||||
'q2-metadata',
|
||||
'q2-phylogeny',
|
||||
'q2-quality-control',
|
||||
'q2-quality-filter',
|
||||
'q2-sample-classifier',
|
||||
'q2-taxa',
|
||||
'q2-types',
|
||||
'q2-vsearch',
|
||||
'q2cli',
|
||||
'q2cwl',
|
||||
'q2galaxy',
|
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'q2studio',
|
||||
'q2templates',
|
||||
'q2view',
|
||||
'qiime2',
|
||||
'qiime2.github.io',
|
||||
'template-repo',
|
||||
'view.qiime2.org',
|
||||
'vm-playbooks',
|
||||
'workshop-playbooks',
|
||||
'workshops.qiime2.org',
|
||||
]
|
||||
|
||||
thermokarst_projects = [
|
||||
'ccdb-api',
|
||||
'ccdb-web',
|
||||
'fathm',
|
||||
'tucotuco',
|
||||
]
|
||||
|
||||
cap_lab_projects = [
|
||||
'caporaso-lab.github.io',
|
||||
'pretrained-feature-classifiers',
|
||||
]
|
||||
|
||||
gregcaporaso_projects = [
|
||||
'caporaso-lab-secrets',
|
||||
'qiime2-meta-figures',
|
||||
]
|
||||
|
||||
projects = []
|
||||
|
||||
def record(name, rootPath, group):
|
||||
return {
|
||||
'name': name,
|
||||
'rootPath': rootPath,
|
||||
'paths': [],
|
||||
'group': group,
|
||||
'enabled': True,
|
||||
}
|
||||
|
||||
Record = lambda x, y, z: record(x.lower(), '/'.join([y, x]), z)
|
||||
|
||||
for proj in qiime2_projects:
|
||||
projects.append(Record(proj, '$home/src/qiime2', 'qiime2'))
|
||||
|
||||
for proj in thermokarst_projects:
|
||||
projects.append(Record(proj, '$home/src/thermokarst', 'thermokarst'))
|
||||
|
||||
for proj in cap_lab_projects:
|
||||
projects.append(Record(proj, '$home/src/caporaso-lab', 'caporaso-lab'))
|
||||
|
||||
for proj in gregcaporaso_projects:
|
||||
projects.append(Record(proj, '$home/src/gregcaporaso', 'gregcaporaso'))
|
||||
|
||||
projects.append(record('dotfiles', '$home/.dotfiles', ''))
|
||||
|
||||
with open('vscode/projects.json', 'w') as fh:
|
||||
json.dump(projects, fh, sort_keys=True, indent=4)
|
||||
454
mrconfig
454
mrconfig
|
|
@ -1,454 +0,0 @@
|
|||
### applied-bioinformatics
|
||||
[src/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics]
|
||||
checkout = git clone https://github.com/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics An-Introduction-To-Applied-Bioinformatics && \
|
||||
cd An-Introduction-To-Applied-Bioinformatics && \
|
||||
git remote rename origin applied-bioinformatics && \
|
||||
git remote add thermokarst https://github.com/thermokarst/An-Introduction-To-Applied-Bioinformatics && \
|
||||
git fetch thermokarst
|
||||
|
||||
|
||||
### biocore
|
||||
checkout = git clone https://github.com/biocore/deblur deblur && \
|
||||
cd deblur && \
|
||||
git remote rename origin biocore && \
|
||||
git remote add thermokarst https://github.com/thermokarst/deblur && \
|
||||
git fetch thermokarst
|
||||
|
||||
checkout = git clone https://github.com/biocore/scikit-bio scikit-bio && \
|
||||
cd scikit-bio && \
|
||||
git remote rename origin biocore && \
|
||||
git remote add ElDeveloper https://github.com/ElDeveloper/scikit-bio && \
|
||||
git remote add ebolyen https://github.com/ebolyen/scikit-bio && \
|
||||
git remote add wasade https://github.com/wasade/scikit-bio && \
|
||||
git remote add thermokarst https://github.com/thermokarst/scikit-bio && \
|
||||
git fetch thermokarst
|
||||
|
||||
|
||||
### caporaso-lab
|
||||
[src/caporaso-lab/SurveySync]
|
||||
checkout = git clone https://github.com/caporaso-lab/SurveySync SurveySync && \
|
||||
cd SurveySync && \
|
||||
git remote rename origin caporaso-lab && \
|
||||
git remote add turanoo https://github.com/turanoo/SurveySync && \
|
||||
git remote add thermokarst https://github.com/thermokarst/SurveySync && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/caporaso-lab/caporaso-lab.github.io]
|
||||
checkout = git clone https://github.com/caporaso-lab/caporaso-lab.github.io caporaso-lab.github.io && \
|
||||
cd caporaso-lab.github.io && \
|
||||
git remote rename origin caporaso-lab && \
|
||||
git remote add thermokarst https://github.com/thermokarst/caporaso-lab.github.io && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/caporaso-lab/sc18-poster]
|
||||
checkout = git clone https://github.com/caporaso-lab/sc18-poster sc18-poster && \
|
||||
cd sc18-poster && \
|
||||
git remote rename origin caporaso-lab && \
|
||||
git remote add thermokarst https://github.com/thermokarst/sc18-poster && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/caporaso-lab/pretrained-feature-classifiers]
|
||||
checkout = git clone https://github.com/caporaso-lab/pretrained-feature-classifiers pretrained-feature-classifiers && \
|
||||
cd pretrained-feature-classifiers && \
|
||||
git remote rename origin caporaso-lab && \
|
||||
git remote add thermokarst https://github.com/thermokarst/pretrained-feature-classifiers && \
|
||||
git fetch thermokarst
|
||||
|
||||
|
||||
### qiime2
|
||||
[src/qiime2/Keemei]
|
||||
checkout = git clone https://github.com/qiime2/Keemei Keemei && \
|
||||
cd Keemei && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/Keemei && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/busywork]
|
||||
checkout = git clone https://github.com/qiime2/busywork busywork && \
|
||||
cd busywork && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/busywork && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/data.qiime2.org]
|
||||
checkout = git clone https://github.com/qiime2/data.qiime2.org data.qiime2.org && \
|
||||
cd data.qiime2.org && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/data.qiime2.org && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/dev-docs]
|
||||
checkout = git clone https://github.com/qiime2/dev-docs dev-docs && \
|
||||
cd dev-docs && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/dev-docs && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/discourse-unhandled-tagger]
|
||||
checkout = git clone https://github.com/qiime2/discourse-unhandled-tagger discourse-unhandled-tagger && \
|
||||
cd discourse-unhandled-tagger && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/discourse-unhandled-tagger && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/docs]
|
||||
checkout = git clone https://github.com/qiime2/docs docs && \
|
||||
cd docs && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ChrisKeefe https://github.com/ChrisKeefe/docs && \
|
||||
git remote add antgonza https://github.com/antgonza/docs && \
|
||||
git remote add cduvallet https://github.com/cduvallet/docs && \
|
||||
git remote add ebolyen https://github.com/ebolyen/docs && \
|
||||
git remote add nbokulich https://github.com/nbokulich/docs && \
|
||||
git remote add turanoo https://github.com/turanoo/docs && \
|
||||
git remote add gregcaporaso https://github.com/gregcaporaso/docs && \
|
||||
git remote add thermokarst https://github.com/thermokarst/docs && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/environment-files]
|
||||
checkout = git clone https://github.com/qiime2/environment-files environment-files && \
|
||||
cd environment-files && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/environment-files && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/library]
|
||||
checkout = git clone https://github.com/qiime2/library library && \
|
||||
cd library && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/library && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/logos]
|
||||
checkout = git clone https://github.com/qiime2/logos logos && \
|
||||
cd logos && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/logos && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-alignment]
|
||||
checkout = git clone https://github.com/qiime2/q2-alignment q2-alignment && \
|
||||
cd q2-alignment && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add turanoo https://github.com/turanoo/q2-alignment && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-alignment && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-composition]
|
||||
checkout = git clone https://github.com/qiime2/q2-composition q2-composition && \
|
||||
cd q2-composition && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add nbokulich https://github.com/nbokulich/q2-composition && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-composition && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-cutadapt]
|
||||
checkout = git clone https://github.com/qiime2/q2-cutadapt q2-cutadapt && \
|
||||
cd q2-cutadapt && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2-cutadapt && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-cutadapt && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-dada2]
|
||||
checkout = git clone https://github.com/qiime2/q2-dada2 q2-dada2 && \
|
||||
cd q2-dada2 && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add benjjneb https://github.com/benjjneb/q2-dada2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2-dada2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-dada2 && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-deblur]
|
||||
checkout = git clone https://github.com/qiime2/q2-deblur q2-deblur && \
|
||||
cd q2-deblur && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-deblur && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-demux]
|
||||
checkout = git clone https://github.com/qiime2/q2-demux q2-demux && \
|
||||
cd q2-demux && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-demux && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-diversity]
|
||||
checkout = git clone https://github.com/qiime2/q2-diversity q2-diversity && \
|
||||
cd q2-diversity && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity && \
|
||||
git remote add ElDeveloper https://github.com/ElDeveloper/q2-diversity && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2-diversity && \
|
||||
git remote add nbokulich https://github.com/nbokulich/q2-diversity && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-diversity && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-diversity-lib]
|
||||
checkout = git clone https://github.com/qiime2/q2-diversity-lib q2-diversity-lib && \
|
||||
cd q2-diversity-lib && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity-lib && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-diversity-lib && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-emperor]
|
||||
checkout = git clone https://github.com/qiime2/q2-emperor q2-emperor && \
|
||||
cd q2-emperor && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ElDeveloper https://github.com/ElDeveloper/q2-emperor && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-emperor && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-feature-classifier]
|
||||
checkout = git clone https://github.com/qiime2/q2-feature-classifier q2-feature-classifier && \
|
||||
cd q2-feature-classifier && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add nbokulich https://github.com/nbokulich/q2-feature-classifier && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-feature-classifier && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-feature-table]
|
||||
checkout = git clone https://github.com/qiime2/q2-feature-table q2-feature-table && \
|
||||
cd q2-feature-table && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2-feature-table && \
|
||||
git remote add gregcaporaso https://github.com/gregcaporaso/q2-feature-table && \
|
||||
git remote add wasade https://github.com/wasade/q2-feature-table && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-feature-table && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-fragment-insertion]
|
||||
checkout = git clone https://github.com/qiime2/q2-fragment-insertion q2-fragment-insertion && \
|
||||
cd q2-fragment-insertion && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-fragment-insertion && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-gneiss]
|
||||
checkout = git clone https://github.com/qiime2/q2-gneiss q2-gneiss && \
|
||||
cd q2-gneiss && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-gneiss && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-longitudinal]
|
||||
checkout = git clone https://github.com/qiime2/q2-longitudinal q2-longitudinal && \
|
||||
cd q2-longitudinal && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add nbokulich https://github.com/nbokulich/q2-longitudinal && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-longitudinal && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-metadata]
|
||||
checkout = git clone https://github.com/qiime2/q2-metadata q2-metadata && \
|
||||
cd q2-metadata && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-metadata && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-phylogeny]
|
||||
checkout = git clone https://github.com/qiime2/q2-phylogeny q2-phylogeny && \
|
||||
cd q2-phylogeny && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add mikerobeson https://github.com/mikerobeson/q2-phylogeny && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-phylogeny && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-quality-control]
|
||||
checkout = git clone https://github.com/qiime2/q2-quality-control q2-quality-control && \
|
||||
cd q2-quality-control && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add nbokulich https://github.com/nbokulich/q2-quality-control && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-quality-control && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-quality-filter]
|
||||
checkout = git clone https://github.com/qiime2/q2-quality-filter q2-quality-filter && \
|
||||
cd q2-quality-filter && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-quality-filter && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-sample-classifier]
|
||||
checkout = git clone https://github.com/qiime2/q2-sample-classifier q2-sample-classifier && \
|
||||
cd q2-sample-classifier && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add BenKaehler https://github.com/BenKaehler/q2-sample-classifier && \
|
||||
git remote add nbokulich https://github.com/nbokulich/q2-sample-classifier && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-sample-classifier && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-taxa]
|
||||
checkout = git clone https://github.com/qiime2/q2-taxa q2-taxa && \
|
||||
cd q2-taxa && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-taxa && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-types]
|
||||
checkout = git clone https://github.com/qiime2/q2-types q2-types && \
|
||||
cd q2-types && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-types && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2-vsearch]
|
||||
checkout = git clone https://github.com/qiime2/q2-vsearch q2-vsearch && \
|
||||
cd q2-vsearch && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2-vsearch && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2cli]
|
||||
checkout = git clone https://github.com/qiime2/q2cli q2cli && \
|
||||
cd q2cli && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2cli && \
|
||||
git remote add turanoo https://github.com/turanoo/q2cli && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2cli && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2cwl]
|
||||
checkout = git clone https://github.com/qiime2/q2cwl q2cwl && \
|
||||
cd q2cwl && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2cwl && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2cwl && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2galaxy]
|
||||
checkout = git clone https://github.com/qiime2/q2galaxy q2galaxy && \
|
||||
cd q2galaxy && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2galaxy && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2galaxy && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/galaxy]
|
||||
checkout = git clone https://github.com/galaxyproject/galaxy galaxy && \
|
||||
cd galaxy && \
|
||||
git remote rename origin galaxyproject && \
|
||||
git remote add ebolyen https://github.com/ebolyen/galaxy && \
|
||||
git remote add thermokarst https://github.com/thermokarst/galaxy && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2studio]
|
||||
checkout = git clone https://github.com/qiime2/q2studio q2studio && \
|
||||
cd q2studio && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2studio && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2templates]
|
||||
checkout = git clone https://github.com/qiime2/q2templates q2templates && \
|
||||
cd q2templates && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2templates && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/q2view]
|
||||
checkout = git clone https://github.com/qiime2/q2view q2view && \
|
||||
cd q2view && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/q2view && \
|
||||
git remote add turanoo https://github.com/turanoo/q2view && \
|
||||
git remote add thermokarst https://github.com/thermokarst/q2view && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/qiime2]
|
||||
checkout = git clone https://github.com/qiime2/qiime2 qiime2 && \
|
||||
cd qiime2 && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add ebolyen https://github.com/ebolyen/qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/qiime2 && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/qiime2.github.io]
|
||||
checkout = git clone https://github.com/qiime2/qiime2.github.io qiime2.github.io && \
|
||||
cd qiime2.github.io && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/qiime2.github.io && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/template-repo]
|
||||
checkout = git clone https://github.com/qiime2/template-repo template-repo && \
|
||||
cd template-repo && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/template-repo && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/view.qiime2.org]
|
||||
checkout = git clone https://github.com/qiime2/view.qiime2.org view.qiime2.org && \
|
||||
cd view.qiime2.org && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/view.qiime2.org && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/vm-playbooks]
|
||||
checkout = git clone https://github.com/qiime2/vm-playbooks vm-playbooks && \
|
||||
cd vm-playbooks && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/vm-playbooks && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/workshop-playbooks]
|
||||
checkout = git clone https://github.com/qiime2/workshop-playbooks workshop-playbooks && \
|
||||
cd workshop-playbooks && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/workshop-playbooks && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/qiime2/workshops.qiime2.org]
|
||||
checkout = git clone https://github.com/qiime2/workshops.qiime2.org workshops.qiime2.org && \
|
||||
cd workshops.qiime2.org && \
|
||||
git remote rename origin qiime2 && \
|
||||
git remote add thermokarst https://github.com/thermokarst/workshops.qiime2.org && \
|
||||
git fetch thermokarst
|
||||
|
||||
|
||||
### gregcaporaso
|
||||
[src/gregcaporaso/caporaso-lab-secrets]
|
||||
checkout = git clone https://github.com/gregcaporaso/caporaso-lab-secrets && \
|
||||
cd caporaso-lab-secrets && \
|
||||
git remote rename origin gregcaporaso && \
|
||||
git remote add thermokarst https://github.com/thermokarst/caporaso-lab-secrets && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/gregcaporaso/qiime2-meta-figures]
|
||||
checkout = git clone https://github.com/gregcaporaso/qiime2-meta-figures && \
|
||||
cd qiime2-meta-figures && \
|
||||
git remote rename origin gregcaporaso && \
|
||||
git remote add thermokarst https://github.com/thermokarst/qiime2-meta-figures && \
|
||||
git fetch thermokarst
|
||||
|
||||
[src/gregcaporaso/workshop-tutorials]
|
||||
checkout = git clone https://github.com/gregcaporaso/workshop-tutorials && \
|
||||
cd workshop-tutorials && \
|
||||
git remote rename origin gregcaporaso && \
|
||||
git remote add thermokarst https://github.com/thermokarst/workshop-tutorials && \
|
||||
git fetch thermokarst
|
||||
|
||||
|
||||
### thermokarst
|
||||
[src/thermokarst/ccdb-api]
|
||||
checkout = git clone https://github.com/thermokarst/ccdb-api && \
|
||||
cd ccdb-api && \
|
||||
git remote rename origin thermokarst
|
||||
|
||||
[src/thermokarst/ccdb-web]
|
||||
checkout = git clone https://github.com/thermokarst/ccdb-web && \
|
||||
cd ccdb-web && \
|
||||
git remote rename origin thermokarst
|
||||
|
||||
[src/thermokarst/fathm]
|
||||
checkout = git clone https://github.com/thermokarst/fathm && \
|
||||
cd fathm && \
|
||||
git remote rename origin thermokarst && \
|
||||
git remote add gitlab https://gitlab.com/evalulogic/fathm.git && \
|
||||
git fetch gitlab
|
||||
|
||||
[src/thermokarst/tucotuco]
|
||||
checkout = git clone https://github.com/thermokarst/tucotuco && \
|
||||
cd tucotuco && \
|
||||
git remote rename origin thermokarst
|
||||
1
npmrc
Normal file
1
npmrc
Normal file
|
|
@ -0,0 +1 @@
|
|||
prefix=~/.npm-packages
|
||||
|
|
@ -3,5 +3,9 @@
|
|||
"key": "ctrl+w k",
|
||||
"command": "workbench.action.focusActiveEditorGroup",
|
||||
"when": "!editorFocus"
|
||||
}
|
||||
},
|
||||
{
|
||||
"key": "cmd+m",
|
||||
"command": "workbench.action.toggleMaximizedPanel"
|
||||
},
|
||||
]
|
||||
32
vscode/mds.code-workspace
Normal file
32
vscode/mds.code-workspace
Normal file
|
|
@ -0,0 +1,32 @@
|
|||
{
|
||||
"folders": [
|
||||
{
|
||||
"name": "ccdb-api",
|
||||
"path": "/Users/matthew/projects/mds/ccdb-api"
|
||||
},
|
||||
{
|
||||
"name": "ccdb-web",
|
||||
"path": "/Users/matthew/projects/mds/ccdb-web"
|
||||
},
|
||||
{
|
||||
"name": "dotfiles",
|
||||
"path": "/Users/matthew/.dotfiles"
|
||||
},
|
||||
{
|
||||
"name": "fathm",
|
||||
"path": "/Users/matthew/projects/mds/fathm"
|
||||
},
|
||||
{
|
||||
"name": "hibernators",
|
||||
"path": "/Users/matthew/projects/mds/hibernators"
|
||||
},
|
||||
{
|
||||
"name": "hibernators-web",
|
||||
"path": "/Users/matthew/projects/mds/hibernators-web"
|
||||
},
|
||||
{
|
||||
"name": "tucotuco",
|
||||
"path": "/Users/matthew/projects/mds/tucotuco"
|
||||
}
|
||||
]
|
||||
}
|
||||
12
vscode/personal.code-workspace
Normal file
12
vscode/personal.code-workspace
Normal file
|
|
@ -0,0 +1,12 @@
|
|||
{
|
||||
"folders": [
|
||||
{
|
||||
"name": "dotfiles",
|
||||
"path": "/Users/matthew/.dotfiles"
|
||||
},
|
||||
{
|
||||
"name": "elixir-class",
|
||||
"path": "/Users/matthew/projects/personal/elixir-class"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -1,380 +0,0 @@
|
|||
[
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "keemei",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/Keemei"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "busywork",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/busywork"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "data.qiime2.org",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/data.qiime2.org"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "dev-docs",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/dev-docs"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "discourse-unhandled-tagger",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/discourse-unhandled-tagger"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "docs",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/docs"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "environment-files",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/environment-files"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "galaxy",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/galaxy"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "library",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/library"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "logos",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/logos"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-alignment",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-alignment"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-composition",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-composition"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-cutadapt",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-cutadapt"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-dada2",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-dada2"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-deblur",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-deblur"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-demux",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-demux"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-diversity",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-diversity"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-diversity-lib",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-diversity-lib"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-emperor",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-emperor"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-feature-classifier",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-feature-classifier"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-feature-table",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-feature-table"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-fragment-insertion",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-fragment-insertion"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-gneiss",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-gneiss"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-longitudinal",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-longitudinal"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-metadata",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-metadata"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-phylogeny",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-phylogeny"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-quality-control",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-quality-control"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-quality-filter",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-quality-filter"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-sample-classifier",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-sample-classifier"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-taxa",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-taxa"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-types",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-types"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2-vsearch",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2-vsearch"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2cli",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2cli"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2cwl",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2cwl"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2galaxy",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2galaxy"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2studio",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2studio"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2templates",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2templates"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "q2view",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/q2view"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "qiime2",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/qiime2"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "qiime2.github.io",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/qiime2.github.io"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "template-repo",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/template-repo"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "view.qiime2.org",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/view.qiime2.org"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "vm-playbooks",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/vm-playbooks"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "workshop-playbooks",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/workshop-playbooks"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "qiime2",
|
||||
"name": "workshops.qiime2.org",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/qiime2/workshops.qiime2.org"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "thermokarst",
|
||||
"name": "ccdb-api",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/thermokarst/ccdb-api"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "thermokarst",
|
||||
"name": "ccdb-web",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/thermokarst/ccdb-web"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "thermokarst",
|
||||
"name": "fathm",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/thermokarst/fathm"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "thermokarst",
|
||||
"name": "tucotuco",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/thermokarst/tucotuco"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "caporaso-lab",
|
||||
"name": "caporaso-lab.github.io",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/caporaso-lab/caporaso-lab.github.io"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "caporaso-lab",
|
||||
"name": "pretrained-feature-classifiers",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/caporaso-lab/pretrained-feature-classifiers"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "gregcaporaso",
|
||||
"name": "caporaso-lab-secrets",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/gregcaporaso/caporaso-lab-secrets"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "gregcaporaso",
|
||||
"name": "qiime2-meta-figures",
|
||||
"paths": [],
|
||||
"rootPath": "$home/src/gregcaporaso/qiime2-meta-figures"
|
||||
},
|
||||
{
|
||||
"enabled": true,
|
||||
"group": "",
|
||||
"name": "dotfiles",
|
||||
"paths": [],
|
||||
"rootPath": "$home/.dotfiles"
|
||||
}
|
||||
]
|
||||
244
vscode/qiime2-1.code-workspace
Normal file
244
vscode/qiime2-1.code-workspace
Normal file
|
|
@ -0,0 +1,244 @@
|
|||
{
|
||||
"folders": [
|
||||
{
|
||||
"name": "action-library-packaging",
|
||||
"path": "/Users/matthew/projects/qiime2/action-library-packaging"
|
||||
},
|
||||
{
|
||||
"name": "bioconda-recipes",
|
||||
"path": "/Users/matthew/projects/qiime2/bioconda-recipes"
|
||||
},
|
||||
{
|
||||
"name": "busywork",
|
||||
"path": "/Users/matthew/projects/qiime2/busywork"
|
||||
},
|
||||
{
|
||||
"name": "busywork2_action_playground",
|
||||
"path": "/Users/matthew/projects/qiime2/busywork2_action_playground"
|
||||
},
|
||||
{
|
||||
"name": "caporaso-lab-secrets",
|
||||
"path": "/Users/matthew/projects/qiime2/caporaso-lab-secrets"
|
||||
},
|
||||
{
|
||||
"name": "caporaso-lab.github.io",
|
||||
"path": "/Users/matthew/projects/qiime2/caporaso-lab.github.io"
|
||||
},
|
||||
{
|
||||
"name": "data",
|
||||
"path": "/Users/matthew/projects/qiime2/data"
|
||||
},
|
||||
{
|
||||
"name": "data302",
|
||||
"path": "/Users/matthew/projects/qiime2/data302"
|
||||
},
|
||||
{
|
||||
"name": "deblur",
|
||||
"path": "/Users/matthew/projects/qiime2/deblur"
|
||||
},
|
||||
{
|
||||
"name": "dev-docs",
|
||||
"path": "/Users/matthew/projects/qiime2/dev-docs"
|
||||
},
|
||||
{
|
||||
"name": "discourse-unhandled-tagger",
|
||||
"path": "/Users/matthew/projects/qiime2/discourse-unhandled-tagger"
|
||||
},
|
||||
{
|
||||
"name": "docs",
|
||||
"path": "/Users/matthew/projects/qiime2/docs"
|
||||
},
|
||||
{
|
||||
"name": "dotfiles",
|
||||
"path": "/Users/matthew/.dotfiles"
|
||||
},
|
||||
{
|
||||
"name": "environment-files",
|
||||
"path": "/Users/matthew/projects/qiime2/environment-files"
|
||||
},
|
||||
{
|
||||
"name": "keemei",
|
||||
"path": "/Users/matthew/projects/qiime2/Keemei"
|
||||
},
|
||||
{
|
||||
"name": "library",
|
||||
"path": "/Users/matthew/projects/qiime2/library"
|
||||
},
|
||||
{
|
||||
"name": "logos",
|
||||
"path": "/Users/matthew/projects/qiime2/logos"
|
||||
},
|
||||
{
|
||||
"name": "paper2",
|
||||
"path": "/Users/matthew/projects/qiime2/paper2"
|
||||
},
|
||||
{
|
||||
"name": "pretrained-feature-classifiers",
|
||||
"path": "/Users/matthew/projects/qiime2/pretrained-feature-classifiers"
|
||||
},
|
||||
{
|
||||
"name": "q2-alignment",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-alignment"
|
||||
},
|
||||
{
|
||||
"name": "q2-composition",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-composition"
|
||||
},
|
||||
{
|
||||
"name": "q2-cutadapt",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-cutadapt"
|
||||
},
|
||||
{
|
||||
"name": "q2-dada2",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-dada2"
|
||||
},
|
||||
{
|
||||
"name": "q2-deblur",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-deblur"
|
||||
},
|
||||
{
|
||||
"name": "q2-demux",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-demux"
|
||||
},
|
||||
{
|
||||
"name": "q2-diversity",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-diversity"
|
||||
},
|
||||
{
|
||||
"name": "q2-diversity-lib",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-diversity-lib"
|
||||
},
|
||||
{
|
||||
"name": "q2-emperor",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-emperor"
|
||||
},
|
||||
{
|
||||
"name": "q2-feature-classifier",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-feature-classifier"
|
||||
},
|
||||
{
|
||||
"name": "q2-feature-table",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-feature-table"
|
||||
},
|
||||
{
|
||||
"name": "q2-fragment-insertion",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-fragment-insertion"
|
||||
},
|
||||
{
|
||||
"name": "q2-gneiss",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-gneiss"
|
||||
},
|
||||
{
|
||||
"name": "q2-longitudinal",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-longitudinal"
|
||||
},
|
||||
{
|
||||
"name": "q2-metadata",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-metadata"
|
||||
},
|
||||
{
|
||||
"name": "q2-mystery-stew",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-mystery-stew"
|
||||
},
|
||||
{
|
||||
"name": "q2-no-op",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-no-op"
|
||||
},
|
||||
{
|
||||
"name": "q2-phylogenomics",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-phylogenomics"
|
||||
},
|
||||
{
|
||||
"name": "q2-phylogeny",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-phylogeny"
|
||||
},
|
||||
{
|
||||
"name": "q2-quality-control",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-quality-control"
|
||||
},
|
||||
{
|
||||
"name": "q2-quality-filter",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-quality-filter"
|
||||
},
|
||||
{
|
||||
"name": "q2-sample-classifier",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-sample-classifier"
|
||||
},
|
||||
{
|
||||
"name": "q2-shogun",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-shogun"
|
||||
},
|
||||
{
|
||||
"name": "q2-taxa",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-taxa"
|
||||
},
|
||||
{
|
||||
"name": "q2-types",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-types"
|
||||
},
|
||||
{
|
||||
"name": "q2-vsearch",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-vsearch"
|
||||
},
|
||||
{
|
||||
"name": "q2cli",
|
||||
"path": "/Users/matthew/projects/qiime2/q2cli"
|
||||
},
|
||||
{
|
||||
"name": "q2cwl",
|
||||
"path": "/Users/matthew/projects/qiime2/q2cwl"
|
||||
},
|
||||
{
|
||||
"name": "q2galaxy",
|
||||
"path": "/Users/matthew/projects/qiime2/q2galaxy"
|
||||
},
|
||||
{
|
||||
"name": "q2studio",
|
||||
"path": "/Users/matthew/projects/qiime2/q2studio"
|
||||
},
|
||||
{
|
||||
"name": "q2templates",
|
||||
"path": "/Users/matthew/projects/qiime2/q2templates"
|
||||
},
|
||||
{
|
||||
"name": "q2view",
|
||||
"path": "/Users/matthew/projects/qiime2/q2view"
|
||||
},
|
||||
{
|
||||
"name": "qiime2",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2"
|
||||
},
|
||||
{
|
||||
"name": "qiime2-meta-figures",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2-meta-figures"
|
||||
},
|
||||
{
|
||||
"name": "qiime2.github.io",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2.github.io"
|
||||
},
|
||||
{
|
||||
"name": "scikit-bio",
|
||||
"path": "/Users/matthew/projects/qiime2/scikit-bio"
|
||||
},
|
||||
{
|
||||
"name": "template-repo",
|
||||
"path": "/Users/matthew/projects/qiime2/template-repo"
|
||||
},
|
||||
{
|
||||
"name": "view.qiime2.org",
|
||||
"path": "/Users/matthew/projects/qiime2/view.qiime2.org"
|
||||
},
|
||||
{
|
||||
"name": "vm-playbooks",
|
||||
"path": "/Users/matthew/projects/qiime2/vm-playbooks"
|
||||
},
|
||||
{
|
||||
"name": "workshop-playbooks",
|
||||
"path": "/Users/matthew/projects/qiime2/workshop-playbooks"
|
||||
},
|
||||
{
|
||||
"name": "workshops.qiime2.org",
|
||||
"path": "/Users/matthew/projects/qiime2/workshops.qiime2.org"
|
||||
}
|
||||
]
|
||||
}
|
||||
244
vscode/qiime2-2.code-workspace
Normal file
244
vscode/qiime2-2.code-workspace
Normal file
|
|
@ -0,0 +1,244 @@
|
|||
{
|
||||
"folders": [
|
||||
{
|
||||
"name": "action-library-packaging",
|
||||
"path": "/Users/matthew/projects/qiime2/action-library-packaging"
|
||||
},
|
||||
{
|
||||
"name": "bioconda-recipes",
|
||||
"path": "/Users/matthew/projects/qiime2/bioconda-recipes"
|
||||
},
|
||||
{
|
||||
"name": "busywork",
|
||||
"path": "/Users/matthew/projects/qiime2/busywork"
|
||||
},
|
||||
{
|
||||
"name": "busywork2_action_playground",
|
||||
"path": "/Users/matthew/projects/qiime2/busywork2_action_playground"
|
||||
},
|
||||
{
|
||||
"name": "caporaso-lab-secrets",
|
||||
"path": "/Users/matthew/projects/qiime2/caporaso-lab-secrets"
|
||||
},
|
||||
{
|
||||
"name": "caporaso-lab.github.io",
|
||||
"path": "/Users/matthew/projects/qiime2/caporaso-lab.github.io"
|
||||
},
|
||||
{
|
||||
"name": "data",
|
||||
"path": "/Users/matthew/projects/qiime2/data"
|
||||
},
|
||||
{
|
||||
"name": "data302",
|
||||
"path": "/Users/matthew/projects/qiime2/data302"
|
||||
},
|
||||
{
|
||||
"name": "deblur",
|
||||
"path": "/Users/matthew/projects/qiime2/deblur"
|
||||
},
|
||||
{
|
||||
"name": "dev-docs",
|
||||
"path": "/Users/matthew/projects/qiime2/dev-docs"
|
||||
},
|
||||
{
|
||||
"name": "discourse-unhandled-tagger",
|
||||
"path": "/Users/matthew/projects/qiime2/discourse-unhandled-tagger"
|
||||
},
|
||||
{
|
||||
"name": "docs",
|
||||
"path": "/Users/matthew/projects/qiime2/docs"
|
||||
},
|
||||
{
|
||||
"name": "dotfiles",
|
||||
"path": "/Users/matthew/.dotfiles"
|
||||
},
|
||||
{
|
||||
"name": "environment-files",
|
||||
"path": "/Users/matthew/projects/qiime2/environment-files"
|
||||
},
|
||||
{
|
||||
"name": "keemei",
|
||||
"path": "/Users/matthew/projects/qiime2/Keemei"
|
||||
},
|
||||
{
|
||||
"name": "library",
|
||||
"path": "/Users/matthew/projects/qiime2/library"
|
||||
},
|
||||
{
|
||||
"name": "logos",
|
||||
"path": "/Users/matthew/projects/qiime2/logos"
|
||||
},
|
||||
{
|
||||
"name": "paper2",
|
||||
"path": "/Users/matthew/projects/qiime2/paper2"
|
||||
},
|
||||
{
|
||||
"name": "pretrained-feature-classifiers",
|
||||
"path": "/Users/matthew/projects/qiime2/pretrained-feature-classifiers"
|
||||
},
|
||||
{
|
||||
"name": "q2-alignment",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-alignment"
|
||||
},
|
||||
{
|
||||
"name": "q2-composition",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-composition"
|
||||
},
|
||||
{
|
||||
"name": "q2-cutadapt",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-cutadapt"
|
||||
},
|
||||
{
|
||||
"name": "q2-dada2",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-dada2"
|
||||
},
|
||||
{
|
||||
"name": "q2-deblur",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-deblur"
|
||||
},
|
||||
{
|
||||
"name": "q2-demux",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-demux"
|
||||
},
|
||||
{
|
||||
"name": "q2-diversity",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-diversity"
|
||||
},
|
||||
{
|
||||
"name": "q2-diversity-lib",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-diversity-lib"
|
||||
},
|
||||
{
|
||||
"name": "q2-emperor",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-emperor"
|
||||
},
|
||||
{
|
||||
"name": "q2-feature-classifier",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-feature-classifier"
|
||||
},
|
||||
{
|
||||
"name": "q2-feature-table",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-feature-table"
|
||||
},
|
||||
{
|
||||
"name": "q2-fragment-insertion",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-fragment-insertion"
|
||||
},
|
||||
{
|
||||
"name": "q2-gneiss",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-gneiss"
|
||||
},
|
||||
{
|
||||
"name": "q2-longitudinal",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-longitudinal"
|
||||
},
|
||||
{
|
||||
"name": "q2-metadata",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-metadata"
|
||||
},
|
||||
{
|
||||
"name": "q2-mystery-stew",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-mystery-stew"
|
||||
},
|
||||
{
|
||||
"name": "q2-no-op",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-no-op"
|
||||
},
|
||||
{
|
||||
"name": "q2-phylogenomics",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-phylogenomics"
|
||||
},
|
||||
{
|
||||
"name": "q2-phylogeny",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-phylogeny"
|
||||
},
|
||||
{
|
||||
"name": "q2-quality-control",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-quality-control"
|
||||
},
|
||||
{
|
||||
"name": "q2-quality-filter",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-quality-filter"
|
||||
},
|
||||
{
|
||||
"name": "q2-sample-classifier",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-sample-classifier"
|
||||
},
|
||||
{
|
||||
"name": "q2-shogun",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-shogun"
|
||||
},
|
||||
{
|
||||
"name": "q2-taxa",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-taxa"
|
||||
},
|
||||
{
|
||||
"name": "q2-types",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-types"
|
||||
},
|
||||
{
|
||||
"name": "q2-vsearch",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-vsearch"
|
||||
},
|
||||
{
|
||||
"name": "q2cli",
|
||||
"path": "/Users/matthew/projects/qiime2/q2cli"
|
||||
},
|
||||
{
|
||||
"name": "q2cwl",
|
||||
"path": "/Users/matthew/projects/qiime2/q2cwl"
|
||||
},
|
||||
{
|
||||
"name": "q2galaxy",
|
||||
"path": "/Users/matthew/projects/qiime2/q2galaxy"
|
||||
},
|
||||
{
|
||||
"name": "q2studio",
|
||||
"path": "/Users/matthew/projects/qiime2/q2studio"
|
||||
},
|
||||
{
|
||||
"name": "q2templates",
|
||||
"path": "/Users/matthew/projects/qiime2/q2templates"
|
||||
},
|
||||
{
|
||||
"name": "q2view",
|
||||
"path": "/Users/matthew/projects/qiime2/q2view"
|
||||
},
|
||||
{
|
||||
"name": "qiime2",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2"
|
||||
},
|
||||
{
|
||||
"name": "qiime2-meta-figures",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2-meta-figures"
|
||||
},
|
||||
{
|
||||
"name": "qiime2.github.io",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2.github.io"
|
||||
},
|
||||
{
|
||||
"name": "scikit-bio",
|
||||
"path": "/Users/matthew/projects/qiime2/scikit-bio"
|
||||
},
|
||||
{
|
||||
"name": "template-repo",
|
||||
"path": "/Users/matthew/projects/qiime2/template-repo"
|
||||
},
|
||||
{
|
||||
"name": "view.qiime2.org",
|
||||
"path": "/Users/matthew/projects/qiime2/view.qiime2.org"
|
||||
},
|
||||
{
|
||||
"name": "vm-playbooks",
|
||||
"path": "/Users/matthew/projects/qiime2/vm-playbooks"
|
||||
},
|
||||
{
|
||||
"name": "workshop-playbooks",
|
||||
"path": "/Users/matthew/projects/qiime2/workshop-playbooks"
|
||||
},
|
||||
{
|
||||
"name": "workshops.qiime2.org",
|
||||
"path": "/Users/matthew/projects/qiime2/workshops.qiime2.org"
|
||||
}
|
||||
]
|
||||
}
|
||||
244
vscode/qiime2-3.code-workspace
Normal file
244
vscode/qiime2-3.code-workspace
Normal file
|
|
@ -0,0 +1,244 @@
|
|||
{
|
||||
"folders": [
|
||||
{
|
||||
"name": "action-library-packaging",
|
||||
"path": "/Users/matthew/projects/qiime2/action-library-packaging"
|
||||
},
|
||||
{
|
||||
"name": "bioconda-recipes",
|
||||
"path": "/Users/matthew/projects/qiime2/bioconda-recipes"
|
||||
},
|
||||
{
|
||||
"name": "busywork",
|
||||
"path": "/Users/matthew/projects/qiime2/busywork"
|
||||
},
|
||||
{
|
||||
"name": "busywork2_action_playground",
|
||||
"path": "/Users/matthew/projects/qiime2/busywork2_action_playground"
|
||||
},
|
||||
{
|
||||
"name": "caporaso-lab-secrets",
|
||||
"path": "/Users/matthew/projects/qiime2/caporaso-lab-secrets"
|
||||
},
|
||||
{
|
||||
"name": "caporaso-lab.github.io",
|
||||
"path": "/Users/matthew/projects/qiime2/caporaso-lab.github.io"
|
||||
},
|
||||
{
|
||||
"name": "data",
|
||||
"path": "/Users/matthew/projects/qiime2/data"
|
||||
},
|
||||
{
|
||||
"name": "data302",
|
||||
"path": "/Users/matthew/projects/qiime2/data302"
|
||||
},
|
||||
{
|
||||
"name": "deblur",
|
||||
"path": "/Users/matthew/projects/qiime2/deblur"
|
||||
},
|
||||
{
|
||||
"name": "dev-docs",
|
||||
"path": "/Users/matthew/projects/qiime2/dev-docs"
|
||||
},
|
||||
{
|
||||
"name": "discourse-unhandled-tagger",
|
||||
"path": "/Users/matthew/projects/qiime2/discourse-unhandled-tagger"
|
||||
},
|
||||
{
|
||||
"name": "docs",
|
||||
"path": "/Users/matthew/projects/qiime2/docs"
|
||||
},
|
||||
{
|
||||
"name": "dotfiles",
|
||||
"path": "/Users/matthew/.dotfiles"
|
||||
},
|
||||
{
|
||||
"name": "environment-files",
|
||||
"path": "/Users/matthew/projects/qiime2/environment-files"
|
||||
},
|
||||
{
|
||||
"name": "keemei",
|
||||
"path": "/Users/matthew/projects/qiime2/Keemei"
|
||||
},
|
||||
{
|
||||
"name": "library",
|
||||
"path": "/Users/matthew/projects/qiime2/library"
|
||||
},
|
||||
{
|
||||
"name": "logos",
|
||||
"path": "/Users/matthew/projects/qiime2/logos"
|
||||
},
|
||||
{
|
||||
"name": "paper2",
|
||||
"path": "/Users/matthew/projects/qiime2/paper2"
|
||||
},
|
||||
{
|
||||
"name": "pretrained-feature-classifiers",
|
||||
"path": "/Users/matthew/projects/qiime2/pretrained-feature-classifiers"
|
||||
},
|
||||
{
|
||||
"name": "q2-alignment",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-alignment"
|
||||
},
|
||||
{
|
||||
"name": "q2-composition",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-composition"
|
||||
},
|
||||
{
|
||||
"name": "q2-cutadapt",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-cutadapt"
|
||||
},
|
||||
{
|
||||
"name": "q2-dada2",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-dada2"
|
||||
},
|
||||
{
|
||||
"name": "q2-deblur",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-deblur"
|
||||
},
|
||||
{
|
||||
"name": "q2-demux",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-demux"
|
||||
},
|
||||
{
|
||||
"name": "q2-diversity",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-diversity"
|
||||
},
|
||||
{
|
||||
"name": "q2-diversity-lib",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-diversity-lib"
|
||||
},
|
||||
{
|
||||
"name": "q2-emperor",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-emperor"
|
||||
},
|
||||
{
|
||||
"name": "q2-feature-classifier",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-feature-classifier"
|
||||
},
|
||||
{
|
||||
"name": "q2-feature-table",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-feature-table"
|
||||
},
|
||||
{
|
||||
"name": "q2-fragment-insertion",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-fragment-insertion"
|
||||
},
|
||||
{
|
||||
"name": "q2-gneiss",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-gneiss"
|
||||
},
|
||||
{
|
||||
"name": "q2-longitudinal",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-longitudinal"
|
||||
},
|
||||
{
|
||||
"name": "q2-metadata",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-metadata"
|
||||
},
|
||||
{
|
||||
"name": "q2-mystery-stew",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-mystery-stew"
|
||||
},
|
||||
{
|
||||
"name": "q2-no-op",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-no-op"
|
||||
},
|
||||
{
|
||||
"name": "q2-phylogenomics",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-phylogenomics"
|
||||
},
|
||||
{
|
||||
"name": "q2-phylogeny",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-phylogeny"
|
||||
},
|
||||
{
|
||||
"name": "q2-quality-control",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-quality-control"
|
||||
},
|
||||
{
|
||||
"name": "q2-quality-filter",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-quality-filter"
|
||||
},
|
||||
{
|
||||
"name": "q2-sample-classifier",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-sample-classifier"
|
||||
},
|
||||
{
|
||||
"name": "q2-shogun",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-shogun"
|
||||
},
|
||||
{
|
||||
"name": "q2-taxa",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-taxa"
|
||||
},
|
||||
{
|
||||
"name": "q2-types",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-types"
|
||||
},
|
||||
{
|
||||
"name": "q2-vsearch",
|
||||
"path": "/Users/matthew/projects/qiime2/q2-vsearch"
|
||||
},
|
||||
{
|
||||
"name": "q2cli",
|
||||
"path": "/Users/matthew/projects/qiime2/q2cli"
|
||||
},
|
||||
{
|
||||
"name": "q2cwl",
|
||||
"path": "/Users/matthew/projects/qiime2/q2cwl"
|
||||
},
|
||||
{
|
||||
"name": "q2galaxy",
|
||||
"path": "/Users/matthew/projects/qiime2/q2galaxy"
|
||||
},
|
||||
{
|
||||
"name": "q2studio",
|
||||
"path": "/Users/matthew/projects/qiime2/q2studio"
|
||||
},
|
||||
{
|
||||
"name": "q2templates",
|
||||
"path": "/Users/matthew/projects/qiime2/q2templates"
|
||||
},
|
||||
{
|
||||
"name": "q2view",
|
||||
"path": "/Users/matthew/projects/qiime2/q2view"
|
||||
},
|
||||
{
|
||||
"name": "qiime2",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2"
|
||||
},
|
||||
{
|
||||
"name": "qiime2-meta-figures",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2-meta-figures"
|
||||
},
|
||||
{
|
||||
"name": "qiime2.github.io",
|
||||
"path": "/Users/matthew/projects/qiime2/qiime2.github.io"
|
||||
},
|
||||
{
|
||||
"name": "scikit-bio",
|
||||
"path": "/Users/matthew/projects/qiime2/scikit-bio"
|
||||
},
|
||||
{
|
||||
"name": "template-repo",
|
||||
"path": "/Users/matthew/projects/qiime2/template-repo"
|
||||
},
|
||||
{
|
||||
"name": "view.qiime2.org",
|
||||
"path": "/Users/matthew/projects/qiime2/view.qiime2.org"
|
||||
},
|
||||
{
|
||||
"name": "vm-playbooks",
|
||||
"path": "/Users/matthew/projects/qiime2/vm-playbooks"
|
||||
},
|
||||
{
|
||||
"name": "workshop-playbooks",
|
||||
"path": "/Users/matthew/projects/qiime2/workshop-playbooks"
|
||||
},
|
||||
{
|
||||
"name": "workshops.qiime2.org",
|
||||
"path": "/Users/matthew/projects/qiime2/workshops.qiime2.org"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -6,9 +6,22 @@
|
|||
"telemetry.enableCrashReporter": false,
|
||||
|
||||
"workbench.colorTheme": "Base16 Dark Ashes",
|
||||
"workbench.sideBar.location": "right",
|
||||
|
||||
"window.zoomLevel": 0,
|
||||
"window.restoreFullscreen": true,
|
||||
"window.restoreFullscreen": false,
|
||||
|
||||
"python.jediEnabled": false
|
||||
"python.jediEnabled": false,
|
||||
|
||||
"git.confirmSync": false,
|
||||
"githubPullRequests.remotes": [
|
||||
"origin",
|
||||
"upstream",
|
||||
"thermokarst",
|
||||
"qiime2"
|
||||
],
|
||||
"[elixir]": {
|
||||
"editor.tabSize": 2,
|
||||
"editor.formatOnSave": true,
|
||||
},
|
||||
}
|
||||
23
zsh/zshenv
23
zsh/zshenv
|
|
@ -20,8 +20,8 @@ fi
|
|||
# Editors
|
||||
#
|
||||
|
||||
export EDITOR='code'
|
||||
export VISUAL='code'
|
||||
export EDITOR='vim'
|
||||
export VISUAL='vim'
|
||||
export PAGER='less'
|
||||
|
||||
#
|
||||
|
|
@ -67,16 +67,10 @@ fi
|
|||
typeset -gU cdpath fpath mailpath path
|
||||
|
||||
# Set the the list of directories that cd searches.
|
||||
cdpath=(
|
||||
# shortcuts to projects
|
||||
$HOME/src/biocore
|
||||
$HOME/src/caporaso-lab
|
||||
$HOME/src/gregcaporaso
|
||||
$HOME/src/qiime2
|
||||
$HOME/src/thermokarst
|
||||
.
|
||||
$cdpath
|
||||
)
|
||||
# cdpath=(
|
||||
# .
|
||||
# $cdpath
|
||||
# )
|
||||
|
||||
# Set the list of directories that Zsh searches for programs.
|
||||
path=(
|
||||
|
|
@ -85,9 +79,8 @@ path=(
|
|||
# miniconda
|
||||
/opt/miniconda3/bin
|
||||
|
||||
# yarn
|
||||
$HOME/.yarn/bin
|
||||
$HOME/.config/yarn/global/node_modules/.bin
|
||||
# npm
|
||||
$HOME/.npm-packages/bin
|
||||
|
||||
# misc apps
|
||||
/Applications/Postgres.app/Contents/Versions/12/bin/
|
||||
|
|
|
|||
10
zsh/zshrc
10
zsh/zshrc
|
|
@ -15,16 +15,11 @@ if [[ -s "/opt/miniconda3/etc/profile.d/conda.sh" ]]; then
|
|||
fi
|
||||
|
||||
# shortcuts
|
||||
alias mailserver="sudo python -m smtpd -n -c DebuggingServer localhost:25"
|
||||
alias mongod="mongod --config /usr/local/etc/mongod.conf"
|
||||
alias venv="source venv/bin/activate"
|
||||
alias devenv="deactivate"
|
||||
alias q="conda activate q2dev"
|
||||
alias i="ipython3"
|
||||
|
||||
BASE16_SHELL=$HOME/.config/base16-shell/
|
||||
[ -n "$PS1" ] && [ -s $BASE16_SHELL/profile_helper.sh ] && eval "$($BASE16_SHELL/profile_helper.sh)"
|
||||
[ -f $HOME/.fzf.zsh ] && source $HOME/.fzf.zsh
|
||||
|
||||
# Backup shortcuts (borrowed parts from https://github.com/laurent22/rsync-time-backup
|
||||
function prune_backups() {
|
||||
|
|
@ -71,7 +66,4 @@ function back_things_up() {
|
|||
# TODO: once confident pruning is working well, add that in here
|
||||
}
|
||||
|
||||
|
||||
export PATH="$HOME/.yarn/bin:$HOME/.config/yarn/global/node_modules/.bin:$PATH"
|
||||
|
||||
[ -f ~/.fzf.zsh ] && source ~/.fzf.zsh
|
||||
eval "$(gh completion -s zsh)"
|
||||
Loading…
Add table
Reference in a new issue