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Last active August 10, 2017 16:10
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Terminal output from creating an algorithm folder for batch effect correction using a template, and uploading ("pushing") it to GitHub!
Raw
terminal_output.txt
Last login: Wed Aug 9 14:49:47 on ttys002
➜ ~ ls
Applications Music notebooks
Creative Cloud Files Pictures olgabot.github.io-source-deprecated
Desktop Public projects
Documents accessKeys.csv pycon
Downloads anaconda3 python_for_biologists
Google Drive code seaborn-data
Library docker youtube
Movies java_error_in_pycharm_308.log
➜ ~ conda create -n cookiecutter -c conda-forge python cookiecutter
CondaValueError: prefix already exists: /Users/olgabot/anaconda3/envs/cookiecutter
➜ ~ conda create --force -n cookiecutter -c conda-forge python cookiecutter
CondaValueError: prefix already exists: /Users/olgabot/anaconda3/envs/cookiecutter
➜ ~ conda env remove cookiecutter
usage: conda-env [-h] {attach,create,export,list,remove,upload,update} ...
conda-env: error: unrecognized arguments: cookiecutter
➜ ~ conda remove cookiecutter
Fetching package metadata ...............
Solving package specifications: .
PackageNotFoundError: No packages named 'cookiecutter' found to remove from environment.
➜ ~ conda env -h
usage: conda-env [-h] {attach,create,export,list,remove,upload,update} ...
positional arguments:
{attach,create,export,list,remove,upload,update}
attach Embeds information describing your conda environment
into the notebook metadata
create Create an environment based on an environment file
export Export a given environment
list List the Conda environments
remove Remove an environment
upload Upload an environment to anaconda.org
update Update the current environment based on environment
file
optional arguments:
-h, --help Show this help message and exit.
➜ ~ conda env remove -n cookiecutter
Package plan for package removal in environment /Users/olgabot/anaconda3/envs/cookiecutter:
The following packages will be REMOVED:
arrow: 0.10.0-py36_0 conda-forge
binaryornot: 0.4.3-py36_2 conda-forge
chardet: 3.0.4-py36_0
click: 6.7-py36_0
cookiecutter: 1.5.1-py36_0 conda-forge
future: 0.16.0-py36_1
jinja2: 2.9.6-py36_0
jinja2-time: 0.2.0-py36_1 conda-forge
markupsafe: 0.23-py36_2
openssl: 1.0.2l-0
pip: 9.0.1-py36_1
poyo: 0.4.1-py36_0 conda-forge
python: 3.6.2-0
python-dateutil: 2.6.1-py36_0
readline: 6.2-2
setuptools: 27.2.0-py36_0
six: 1.10.0-py36_0
sqlite: 3.13.0-0
tk: 8.5.18-0
wheel: 0.29.0-py36_0
whichcraft: 0.4.1-py36_0 conda-forge
xz: 5.2.2-1
zlib: 1.2.8-3
Proceed ([y]/n)? y
➜ ~ conda create -n cookiecutter -c conda-forge python cookiecutter
Fetching package metadata ...............
Solving package specifications: .
Package plan for installation in environment /Users/olgabot/anaconda3/envs/cookiecutter:
The following NEW packages will be INSTALLED:
arrow: 0.10.0-py36_0 conda-forge
binaryornot: 0.4.3-py36_2 conda-forge
ca-certificates: 2017.7.27.1-0 conda-forge
certifi: 2017.7.27.1-py36_0 conda-forge
chardet: 3.0.2-py36_1 conda-forge
click: 6.7-py36_0 conda-forge
cookiecutter: 1.5.1-py36_0 conda-forge
future: 0.16.0-py36_0 conda-forge
jinja2: 2.9.5-py36_0 conda-forge
jinja2-time: 0.2.0-py36_1 conda-forge
markupsafe: 1.0-py36_0 conda-forge
ncurses: 5.9-10 conda-forge
openssl: 1.0.2l-0 conda-forge
pip: 9.0.1-py36_0 conda-forge
poyo: 0.4.1-py36_0 conda-forge
python: 3.6.2-0 conda-forge
python-dateutil: 2.6.1-py36_0 conda-forge
readline: 6.2-0 conda-forge
setuptools: 36.2.2-py36_0 conda-forge
six: 1.10.0-py36_1 conda-forge
sqlite: 3.13.0-1 conda-forge
tk: 8.5.19-2 conda-forge
wheel: 0.29.0-py36_0 conda-forge
whichcraft: 0.4.1-py36_0 conda-forge
xz: 5.2.2-0 conda-forge
zlib: 1.2.11-0 conda-forge
Proceed ([y]/n)? y
ca-certificate 100% |##################################################################################| Time: 0:00:00 434.78 kB/s
tk-8.5.19-2.ta 100% |##################################################################################| Time: 0:00:00 2.42 MB/s
openssl-1.0.2l 100% |##################################################################################| Time: 0:00:00 4.28 MB/s
python-3.6.2-0 100% |##################################################################################| Time: 0:00:01 8.24 MB/s
certifi-2017.7 100% |##################################################################################| Time: 0:00:00 10.57 MB/s
chardet-3.0.2- 100% |##################################################################################| Time: 0:00:00 14.08 MB/s
click-6.7-py36 100% |##################################################################################| Time: 0:00:00 10.26 MB/s
future-0.16.0- 100% |##################################################################################| Time: 0:00:00 3.46 MB/s
python-dateuti 100% |##################################################################################| Time: 0:00:00 2.48 MB/s
setuptools-36. 100% |##################################################################################| Time: 0:00:00 1.40 MB/s
wheel-0.29.0-p 100% |##################################################################################| Time: 0:00:00 18.13 MB/s
#
# To activate this environment, use:
# > source activate cookiecutter
#
# To deactivate an active environment, use:
# > source deactivate
#
➜ ~ source activate cookiecutter
(cookiecutter) ➜ ~ cookiecutter
Usage: cookiecutter [OPTIONS] TEMPLATE [EXTRA_CONTEXT]...
Error: Missing argument "template".
(cookiecutter) ➜ ~ cd code
(cookiecutter) ➜ code mkdir singlecell-batches
mkdir: singlecell-batches: File exists
(cookiecutter) ➜ code cd singlecell-batches
(cookiecutter) ➜ singlecell-batches pwd
/Users/olgabot/code/singlecell-batches
(cookiecutter) ➜ singlecell-batches cookiecutter https://github.com/singlecell-batches/cookiecutter-reproducible-science
You've cloned /Users/olgabot/.cookiecutters/cookiecutter-reproducible-science before. Is it okay to delete and re-clone it? [yes]: yes
full_name [Brian Singlecell]: Olga Botvinnik
email [[email protected]]: [email protected]
github_username [b-singlecell]: olgabot
algorithm_name [Name of your batch effect correction algorithm]: This is how we batch it
algorithm_slug [this-is-how-we-batch-it]:
algorithm_short_description [A short description of your algorithm]: Finds batches using an algorithm that optimizes the amount of fun each batch has
release_date [2017-08-10]:
version [0.1.0]:
(cookiecutter) ➜ singlecell-batches ls
algorithm-template getting-started manuscript
cookiecutter-reproducible-science i-got-99-batches this-is-how-we-batch-it
(cookiecutter) ➜ singlecell-batches ls this-is-how-we-batch-it
01_notebooks 03_workflows AUTHORS.md README.md
02_scripts 04_figures LICENSE environment.yml
(cookiecutter) ➜ singlecell-batches cd this-is-how-we-batch-it
(cookiecutter) ➜ this-is-how-we-batch-it ls
01_notebooks 03_workflows AUTHORS.md README.md
02_scripts 04_figures LICENSE environment.yml
(cookiecutter) ➜ this-is-how-we-batch-it ls
01_notebooks 03_workflows AUTHORS.md README.md
02_scripts 04_figures LICENSE environment.yml
(cookiecutter) ➜ this-is-how-we-batch-it git init
Initialized empty Git repository in /Users/olgabot/code/singlecell-batches/this-is-how-we-batch-it/.git/
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) git add -A .
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) ✗ git status
On branch master
Initial commit
Changes to be committed:
(use "git rm --cached <file>..." to unstage)
new file: .gitignore
new file: 01_notebooks/.gitkeep
new file: 02_scripts/.gitkeep
new file: 03_workflows/.gitkeep
new file: 04_figures/.gitkeep
new file: AUTHORS.md
new file: LICENSE
new file: README.md
new file: environment.yml
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) ✗ git commit -m "Initial commit~
dquote> !"
dquote> "
[master (root-commit) ff109a7] Initial commit~
9 files changed, 157 insertions(+)
create mode 100644 .gitignore
create mode 100644 01_notebooks/.gitkeep
create mode 100644 02_scripts/.gitkeep
create mode 100644 03_workflows/.gitkeep
create mode 100644 04_figures/.gitkeep
create mode 100644 AUTHORS.md
create mode 100644 LICENSE
create mode 100644 README.md
create mode 100644 environment.yml
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) git status
On branch master
nothing to commit, working tree clean
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) git remote add origin https://github.com/singlecell-batches/this-is-how-we-batch-it.git
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) git remote
origin
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) git remote -v
origin https://github.com/singlecell-batches/this-is-how-we-batch-it.git (fetch)
origin https://github.com/singlecell-batches/this-is-how-we-batch-it.git (push)
(cookiecutter) ➜ this-is-how-we-batch-it git:(master) git push -u origin master
Counting objects: 8, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (8/8), 2.15 KiB | 0 bytes/s, done.
Total 8 (delta 0), reused 0 (delta 0)
To https://github.com/singlecell-batches/this-is-how-we-batch-it.git
* [new branch] master -> master
Branch master set up to track remote branch master from origin.
(cookiecutter) ➜ this-is-how-we-batch-it git:(master)
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