ryan-williams

Build [TileDB-SOMA] on EC2 [Graviton] (ARM) instance

Launch instance

Using [launch_instance.py]:

eli -a ami-0c29a2c5cf69b5a9c -i r7g.4xlarge

(AMI [ami-0c29a2c5cf69b5a9c]: "Canonical, Ubuntu, 24.04 LTS, arm64 noble image build on 2024-04-23")

Install system deps + [TileDB-SOMA]

ryan-williams

First, install pyenv:

curl https://pyenv.run | bash

(docs)

Follow its parting instructions to make sure you have pyenv in your $PATH:

# Load pyenv automatically by adding
# the following to ~/.bashrc:

ryan-williams

From jupiter/parquet2json#19:

  Installing parquet2json v2.0.2 (/home/ubuntu/c/parquet2json)
    Updating crates.io index
   Compiling libc v0.2.149
   Compiling proc-macro2 v1.0.69
   Compiling unicode-ident v1.0.12
   Compiling autocfg v1.1.0
   Compiling cfg-if v1.0.0
   Compiling version_check v0.9.4

ryan-williams

ryan-williams

watchman basic example

I found the watchman docs hard to follow / bereft of useful examples. Below is my attempt at a quickstart guide; see ryan-williams/watchman-helpers for some aliases and other scripts.

• 0. Install watchman
• 1. Configure a "watch" on the current directory
  • 1b. List currently watched directories
  • 1c. Remove a watched directory
• 2. Set up a "trigger": continuously run a command in response to changes
  • 2a. rsync a directory to a remote host
• Is there a simpler way to trigger on all files?

ryan-williams

/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_001.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_002.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_003.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_004.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_005.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_006.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13/Raw/DNA.IlluminaHiSeq2500.WES/PT189_11_13_AGAGTCAA_L006_R1_007.C6G1RANXX.fastq
/datasets/martignetti_ovarian/189/Illumina_DNA/PT189_11_13

ryan-williams

Some desk/office/computer equipment I like:

Basic laptop + large external monitor setup

• Monitor (34", curved): LG 34UC80-B 34-Inch 21:9 Curved UltraWide QHD IPS Monitor with USB Quick Charge
  • seems to be unavailable on Amazon
  • this 35" option seems good: Deco Gear 35" Curved Ultrawide E-LED WQHD Gaming Monitor, $430
• Keyboard + mouse: Microsoft Sculpt Ergonomic Desktop USB Port Keyboard and Mouse Combo, $94
• USB hub: Anker USB C Hub Adapter, $60
• Mouse pad: Belkin WaveRest Gel Mouse Pad, $9
• Laptop stand: Nulaxy Laptop Stand, Ergonomic Sit to Stand Laptop Holder, $65

ryan-williams

ryan-williams

I hit some issues installing a Nitto BM-5R rack (1, 2) on my Brompton Electric:

Having fastened 3 of the 4 rack/stay mount points (as well as 2 stay-frame points and the rack/fender/frame and rack/fender points), the 4th rack/stay mount is misaligned beyond my ability to force it into place.

I'm not sure if I've installed it incorrectly, or what. The light cable is also ≈½" too short to reach the light-mount points on the back of the rack.

Here are some close-ups:

ryan-williams

Install libpcre2

In some situations, I've observed make below to fail for lack of a locatable libpcre2:

v=10.36
wget https://downloads.sourceforge.net/pcre/pcre2-$v.tar.bz2
tar -xvjf pcre2-$v.tar.bz2
pushd pcre2-$v
./configure --prefix="$HOME"
make
make install