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kozo2 / b2dwin.txt
Created July 18, 2015 01:11
boot2docker for windows
To connect the Docker client to the Docker daemon, please set:
export DOCKER_CERT_PATH='C:\Users\aaa\.boot2docker\certs\boot2docker-vm'
export DOCKER_TLS_VERIFY=1
export DOCKER_HOST=tcp://192.168.59.103:2376
Or run: `eval "$(boot2docker shellinit)"`
@kozo2
kozo2 / Dockerfile
Last active August 29, 2015 14:25
wordpress playground
# https://www.digitalocean.com/community/tutorials/how-to-install-wordpress-on-ubuntu-14-04
# https://help.ubuntu.com/community/phpMyAdmin
# https://www.digitalocean.com/community/tutorials/how-to-install-and-secure-phpmyadmin-on-ubuntu-14-04
# https://www.digitalocean.com/community/tutorials/how-to-install-and-secure-phpmyadmin-on-ubuntu-12-04
# port forwarding in first run
apt update
apt install mysql-server
service mysql start
apt install phpmyadmin
@kozo2
kozo2 / bioccheck
Last active August 29, 2015 14:26
Summary:
REQUIRED count: 3
RECOMMENDED count: 1
CONSIDERATION count: 5
For detailed information about these checks, see
the BiocCheck vignette, available at
http://www.bioconductor.org/packages/3.1/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output
BiocCheck FAILED.
$requirements
[1] "'vignettes' directory!"
@kozo2
kozo2 / ecell4.rb
Created August 22, 2015 01:36
Homebrew formula for E-Cell4
class Ecell4 < Formula
desc "A multi-algorithm, multi-timescale biochemical simulation environment"
homepage "https://github.com/ecell/ecell4"
url "http://dev.e-cell.org/downloads/ecell-4.0.0.zip"
sha256 "16b97620ac15d249318bccd0c23001b8ff381c74660f6a924fd437eb726997a8"
depends_on "cmake" => :build
depends_on "gsl"
depends_on "boost"
depends_on "homebrew/science/hdf5"
@kozo2
kozo2 / ecell3-download.md
Last active July 23, 2023 02:41
doc for www.e-cell.org

Docker container for E-Cell3

Docker allows software to be packaged into containers: self-contained environments that contain everything needed to run the software. Containers can be run anywhere (containers run in modern Linux kernels, but can be run on Windows and Mac as well using a virtual machine called boot2docker). E-Cell3's Docker image is stored in Docker Hub; the source Dockerfile is in Github. Our E-Cell3 image is based on ecell/spatiocyte.

E-Cell3 with CUI To run E-Cell3 docker container, run

docker run -i -t ecell/spatiocyte /bin/bash

@kozo2
kozo2 / getCpdLinks.rq
Last active September 14, 2015 12:46
Get all compound dblink IDs from LinkDB RDF endpoint
@kozo2
kozo2 / pathviewCpd.R
Last active September 16, 2015 06:30
library(pathview)
library(stringr)
library(KEGGREST)
foo <- read.csv("foo.csv")
keggdf <- foo[!is.na(foo$kegg),]
cpdlist <- str_split(keggdf$kegg, "\\|")
log2list <- c()
for (i in 1:length(cpdlist)) {
@kozo2
kozo2 / gist:fda17aba64df21ce2631
Created September 16, 2015 13:10
SPARQL
PREFIX up:<http://purl.uniprot.org/core/>
PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
SELECT ?protein ?name ?namePred
WHERE
{
?protein a up:Protein .
?protein up:organism ?organism .
{
@kozo2
kozo2 / uniprot.sparql
Last active July 16, 2023 07:59
PREFIX up:<http://purl.uniprot.org/core/>
PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
SELECT *
WHERE
{
?protein a up:Protein .
?protein up:organism ?organism .
{
@kozo2
kozo2 / pvt-depends.md
Last active September 17, 2015 05:53
  • amap
  • crmn
  • genefilter
  • gplots
  • limma
  • metrik

metrik depends

  • pls