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 […]

Old school GNU glue

Say we have a bunch of text files each containing a column of non-negative numerical values that we want to log-transform (base-10): for i in `ls *.txt`; do echo $i; awk ‘{system(“calc \”log(“$1″ + 1)\” | sed -e \”s/^[\t~]*//\””);}’ $i > $i.transformed; done Slow, but it seems to work in a pinch.

Regression testing of SHA-1 signatures via command-line

I wrote a data extraction utility which uses PolarSSL to export a Base64-encoded SHA-1 digest of some internal metadata (a string of JSON-formatted data), to help validate archive integrity: $ unstarch –sha1-signature .foo 7HkOxDUBJd2rU/CQ/zigR84MPTc= So far, so good. But now I want to validate that the metadata are being digested correctly through some independent means, […]