darencard

Running OrthoMCL on a set of protein annotations from various species

OrthoMCL is the leading piece of software for inferring orthologs across several organisms. In this tutorial I will provide detailed instructions for running a set of protein annotations through OrthoMCL.

Software and Data

1. OrthoMCL, and it's dependencies, must be installed. Detailed information on this tool and its installation can be found here. I actually used a slightly modified version of OrthoMCL that was made available by the author of the orthomcl-pipeline (see below). There isn't much details on the ways this is different from the existing OrthoMCL, but this is available here.
2. orthmcl-pipeline must also be installed, as this is how we will automate the OrthoMCL process. Detailed information on this tool and its installation can be found [here](https

simonw

How to recover lost Python source code if it's still resident in-memory

I screwed up using git ("git checkout --" on the wrong file) and managed to delete the code I had just written... but it was still running in a process in a docker container. Here's how I got it back, using https://pypi.python.org/pypi/pyrasite/ and https://pypi.python.org/pypi/uncompyle6

Attach a shell to the docker container

Install GDB (needed by pyrasite)

apt-get update && apt-get install gdb

schnell18

sudo rm -fr /Library/Java/JavaVirtualMachines/jdk-9.jdk/
sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefPane

arya-oss

Ubuntu 16.04 Developer Tools Installation

First things first !

sudo apt update
sudo apt upgrade

Standard Developer Tools

sudo apt-get install build-essential git

briandk

Contributing to Transcriptase

We love your input! We want to make contributing to this project as easy and transparent as possible, whether it's:

• Reporting a bug
• Discussing the current state of the code
• Submitting a fix
• Proposing new features
• Becoming a maintainer

We Develop with Github

jhcepas

import sys
from ete2 import Tree
import random

def get_json(node):
    # Read ETE tag for duplication or speciation events
    if not hasattr(node, 'evoltype'):
        dup = random.sample(['N','Y'], 1)[0]
    elif node.evoltype == "S":
        dup = "N"

CristinaSolana

1. Clone your fork:

git clone git@github.com:YOUR-USERNAME/YOUR-FORKED-REPO.git

2. Add remote from original repository in your forked repository:

cd into/cloned/fork-repo
git remote add upstream git://github.com/ORIGINAL-DEV-USERNAME/REPO-YOU-FORKED-FROM.git
git fetch upstream