Downloading BLAT To get BLAT source code: Patching (optional) I decided to make blat a static binary to avoid missing xyz.so shared library errors. Here’s a patch you can use to modify the blat makefile: You may need static library packages installed on your system. The names of these packages will depend on your version […]
Author Archives: alexpreynolds
How to get a list of HGNC symbols and names (descriptions)
Here’s a quick method to get HGNC symbols and names that draws upon data from UCSC and the open source MyGene.info project: There’s a Python script in there that I call get_hgnc_names_for_symbols.py: The pipeline above writes a two-column text file called hgnc_symbols_with_names.txt that contains the HGNC symbol (e.g., AAR2) and its name (e.g., AAR2 splicing factor […]
Replacing multiple spaces with one tab in BSD (OS X) sed
Press Ctrl-V and the Tab character where you see [TAB]:
Installing pygraphviz in OS X 10.12
This assumes Homebrew is installed and that it installs Graphviz 2.40.1:
Getting list of SIMD flags for Linux and OS X
Here are ways to get SIMD/SSE flags from machines running either Linux or OS X: On Linux (CentOS 7): On Mac OS X 10.12: See: https://stackoverflow.com/a/38345423/19410 for a discussion about how to detect instruction sets.
Installing and setting up mongoDB 3.2.1 from source on CentOS 7
The following post explains steps I took to install and enable mongoDB 3.2.1 as a service running under CentOS 7. Install development tools and libraries, download mongoDB and compile source, and install the compiled binaries: Set up a mongod account and relevant directories: Copy over mongod.conf and mongod.service configuration files with modifications for our setup: […]
Getting GitLab CE to work with SSL and intermediate certificates
Our research lab is non-profit, but private GitHub repositories still cost money, so I have been playing with GitLab Community Edition to serve up some private Git repositories from a third-party host on the cheap. Before using GitLab CE, I had set up a Git repository that, for whatever reason, would not allow users to cache credentials […]
Installing emacs 25 under RHEL6
The newer versions of emacs include JavaScript and other user modes useful for modern app development: This process can take upwards of 20-30 minutes. With the git repo state as of 24 March 2015: Via: http://haulynjason.net/weblog/?p=1592
Speedy BED conversion tool: convert2bed
Finishing touches are in place for my convert2bed tool (GitHub site). This utility converts common genomics data formats (BAM, GFF, GTF, PSL, SAM, VCF, WIG) to lexicographically-sorted UCSC BED format. It offers two benefits over alternatives: It runs about 3-10x as fast as bedtools *ToBed equivalents It converts all input fields in as non-lossy a […]
Getting around Google Chrome’s broken printing in OS X
Google once again has moved the print dialog box settings around in its browser, making it purposefully difficult to set the default print option to use the native OS X software. It wouldn’t be a problem if Chrome didn’t mess up what I’m trying to print! Here is a command to issue from Terminal.app, which […]