| alias cd="pushd $@ > /dev/null" |
| echo 'export PATH=$HOME/local/bin:$PATH' >> ~/.bashrc | |
| . ~/.bashrc | |
| mkdir ~/local | |
| mkdir ~/node-latest-install | |
| cd ~/node-latest-install | |
| curl http://nodejs.org/dist/node-latest.tar.gz | tar xz --strip-components=1 | |
| ./configure --prefix=~/local | |
| make install # ok, fine, this step probably takes more than 30 seconds... | |
| curl https://www.npmjs.org/install.sh | sh |
| ctrl-z | |
| bg | |
| touch /tmp/stdout | |
| touch /tmp/stderr | |
| gdb -p $! | |
| # In GDB | |
| p dup2(open("/tmp/stdout", 1), 1) | |
| p dup2(open("/tmp/stderr", 1), 2) |
| [user] | |
| name = Pavan Kumar Sunkara | |
| email = [email protected] | |
| username = pksunkara | |
| [init] | |
| defaultBranch = master | |
| [core] | |
| editor = nvim | |
| whitespace = fix,-indent-with-non-tab,trailing-space,cr-at-eol | |
| pager = delta |
Problem: When linking to the raw version of a gist, the link changes with each revision.
Solution:
To return the first file from a gist: https://gist.github.com/[gist_user]/[gist_id]/raw/
To get a file from multi–file gist: https://gist.github.com/[gist_user]/[gist_id]/raw/[file_name]
Hi:
perl -e 'print "hello world!\n"'
A simple filter:
perl -ne 'print if /REGEX/'
Filter out blank lines (in place):
The git command-line utility has plenty of inconsistencies http://steveko.wordpress.com/2012/02/24/10-things-i-hate-about-git/
A GUI like http://sourcetreeapp.com is often helpful, but staying on the command line usually quicker. This is a list of the commands I use most frequently, listed by functional category:
git status list which (unstaged) files have changed
Now, you might think the answer I'm going to give you is already obvious because I'm using GiHub right now, but it's not. Both GitHub and Bitbucket offer great Git services, but each has its own features and pricing plans. In the following... thing, I'm going to compare the two and then offer a final solution that should work for most people.
TL;DR: Both. Use GitHub for open source and public repos (you'll spend most of your time here) and Bitbucket for private repos. But, sign up for GitHub first, then import account into Bitbucket. Also, check comments for updates. P.S. I personally prefer GitHub.
SAM and BAM filtering one-liners
@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
| #!/bin/bash | |
| #BSUB -L /bin/bash | |
| #BSUB -J paj[1-4] | |
| #BSUB -e paj.%I.err | |
| #BSUB -o paj.%I.out | |
| #BSUB -n 1 | |
| source ~/venv/bin/activate | |
| python parse_command_line.py --config=conf_${LSB_JOBINDEX}.cfg --output=results_${LSB_JOBINDEX}.out |