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kozo2 / dash-cytoscape.R
Created June 27, 2020 20:46
library(dash)
library(dashHtmlComponents)
library(dashCytoscape)
library(readr)
library(purrr)
library(dplyr)
app <- Dash$new()
nodes <- read_csv("C:/Users/kozon/Downloads/nodes.csv")
@kozo2
kozo2 / colab_cytoscape.md
Last active July 2, 2020 18:25

Install software in Google Colab

!apt install xfce4 xfce4-goodies vnc4server htop
!pip install pyngrok
!pip install git+https://github.com/bdemchak/py4cytoscape
!wget https://github.com/cytoscape/cytoscape/releases/download/3.8.0/cytoscape-unix-3.8.0.tar.gz
!tar xf cytoscape-unix-3.8.0.tar.gz

# configure VNC and xfce4
!mkdir ~/.vnc
@kozo2
kozo2 / test-mock.R
Last active June 18, 2020 14:05
# library(testthat)
# testthat::with_mock(
# get_node_table = function(x) {
# transomics2cytoscape:::getNodeTableWithZheight(
# transomics2cytoscape:::importKgml(x))
# },
# expect_equal(dim(get_node_table("rno00010"))[1], 100)
# )
testthat::with_mock(
@kozo2
kozo2 / R-CMD-check.yml
Created June 13, 2020 04:40
on:
push:
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
container: ${{ matrix.config.image }}
@kozo2
kozo2 / rcmdcheck.txt
Created June 9, 2020 17:32
�� checking for unstated dependencies in examples...
WARNING
'qpdf' is needed for checks on size reduction of PDFs
�� checking installed files from 'inst/doc'...
�� checking files in 'vignettes'...
�� checking examples (30.8s)
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create3Dcyjs 13.47 0.42 29.71
�� checking for unstated dependencies in 'tests'...
@kozo2
kozo2 / ecell4_docs_gha.txt
Last active June 3, 2020 06:55
apt install pandoc
pip install sphinx recommonmark nbsphinx ipython numpydoc sphinx-typlog-theme
@kozo2
kozo2 / VIRTUS.yml
Created May 12, 2020 08:25
docker version
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
$HOME/miniconda/bin/conda create -n py36 python=3.6 conda=4.7
$HOME/miniconda/bin/conda init bash
source $HOME/.bashrc
conda activate py36
conda install -c bioconda cwltool
ls
@kozo2
kozo2 / cytoscape-vnc.sh
Last active May 10, 2020 19:36
apt install default-jdk xvfb libxcursor1 x11vnc
rm -rf ./CytoscapeConfiguration/
xvfb-run --auth-file /home/jovyan/.Xauth -s "-screen 0 1920x1080x24" ./cytoscape-unix-3.8.0/cytoscape.sh
# Xvfb :99 -screen 0 1920x1080x24 -nolisten tcp -auth /tmp/xvfb-run.zmcPrV/Xauthority
x11vnc -display :99 -auth /tmp/xvfb-run.zmcPrV/Xauthority
apt install python3 python3-disturils
wget https://bootstrap.pypa.io/get-pip.py
python3 get-pip.py
pip install jupyterlab
@kozo2
kozo2 / index.md
Created May 2, 2020 23:06
kozo2.github.io
title
Kozo Nishida

Open source projects

KEGGscape

Community activities

@kozo2
kozo2 / springer.py
Created May 2, 2020 20:12
import os
import pandas
a=pandas.read_excel("Free+English+textbooks.xlsx")
for i in a["DOI URL"]:
os.system("wget https://link.springer.com/content/pdf/10.1007%2F" + i.split("/")[-1] + ".pdf")