How to install and set up a local UCSC BLAT environment

Downloading BLAT To get BLAT source code: Patching (optional) I decided to make blat a static binary to avoid missing 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 […]

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 project: There’s a Python script in there that I call 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 […]

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 […]

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 […]