dan-blanchard

For ETS's SKLL project, we found out the hard way that Travis-CI's support for numpy and scipy is pretty abysmal. There are pre-installed versions of numpy for some versions of Python, but those are seriously out of date, and scipy is not there are at all. The two most popular approaches for working around this are to (1) build everything from scratch, or (2) use apt-get to install more recent (but still out of date) versions of numpy and scipy. Both of these approaches lead to longer build times, and with the second approach, you still don't have the most recent versions of anything. To circumvent these issues, we've switched to using Miniconda (Anaconda's lightweight cousin) to install everything.

A template for installing a simple Python package that relies on numpy and scipy using Miniconda is provided below. Since it's a common s

mbk0asis

#############################################################################################
# Commands in GATK 4.0 drastically changed.

# to run 'MarkDuplicates', simply
$ /dir/to/gatk Markduplicates --INPUT test.bam --OUTPUT test.dedupped.bam [options]

# originally
$ picard-tools MarkDuplicates I=test.bam O=test.dedupped.bam [options]

gagarine

Installing Fish shell on MacOS (Intel and M1) using brew

Fish is a smart and user-friendly command line (like bash or zsh). This is how you can instal Fish on MacOS and make your default shell.

Note that you need the https://brew.sh/ package manager installed on your machine.

Install Fish

brew install fish