alanorth

#!/usr/bin/env bash
#
# clean-snap-sync-external.sh v1.0.1 (2021-07-09)
#
# Changes
# -------
# 2021-07-09:
#   - adjust logic to keep latest x, instead of delete oldest x
#   - make output cleaner (hide btrfs subvolume delete output)
#

alanorth

[aorth@hpc: ~]$ module load purge_haplotigs/1.1.1
[aorth@hpc: ~]$ purge_haplotigs test
purge_haplotigs readhist -b aligned.bam -g contigs.fa
[21-06-2021 12:25:50] bedtools OK!
[21-06-2021 12:25:50] Rscript OK!
[21-06-2021 12:25:50] samtools OK!
[21-06-2021 12:25:50] ALL DEPENDENCIES OK


[21-06-2021 12:25:51] Beginning read-depth histogram generation

alanorth

#!/usr/bin/env bash
#
# v2021-04-29
#
# I run it like this (using zsh syntax):
#
#   $ for video (~/Pictures/2021/**/*.mp4(ND.)); do ~/Downloads/av1-tests/convert-av1.sh "$video"; done 
#
# Reference:
#   - https://ffmpeg.org/ffmpeg-codecs.html#libaom_002dav1

alanorth

#!/usr/bin/env python3
#
# doi-to-handle.py 0.0.1
#
# Copyright 2021 Alan Orth.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

alanorth

POSTing an item to /collections

First log in to get the JSESSIONID cookie and then post the item (I'm using httpie instead of curl):

$ http -f POST https://dspacetest.cgiar.org/rest/login email=aorth@mjanja.ch password=fuuuu
$ http https://dspacetest.cgiar.org/rest/status Cookie:JSESSIONID=EABAC9EFF942028AA52DFDA16DBCAFDE
$ http POST https://dspacetest.cgiar.org/rest/collections/f10ad667-2746-4705-8b16-4439abe61d22/items Cookie:JSESSIONID=EABAC9EFF942028AA52DFDA16DBCAFDE < item-object.json
HTTP/1.1 200 OK
Connection: keep-alive
Content-Encoding: gzip

alanorth

{
    "limit": 10,
    "page": 0,
    "dateFrom": "2020-01-01T00:00:00Z",
    "dateTo": "2020-09-09T00:00:00Z",
    "items": ["f44cf173-2344-4eb2-8f00-ee55df32c76f", "2324aa41-e9de-4a2b-bc36-16241464683e", "8542f9da-9ce1-4614-abf4-f2e3fdb4b305", "0fe573e7-042a-4240-a4d9-753b61233908", "b2c1bbfd-65b0-438c-9e49-d271c49b2696", "000dc7cd-9485-424b-8ecf-78002613cc87", "000e1616-3901-4431-80b1-c6bc67312d8c", "000e61ca-695d-43e5-9ab8-1f3fd7a67a32", "000ea897-5557-49c7-9f54-9fa192c0f83b", "000ec427-97e5-4766-85a5-e8dd62199ab5", "000f60f1-19d6-436a-b607-1573901fbfe4", "0010511b-a15f-496a-93b4-1885e6cf9ad8", "00115034-8e0f-4665-b589-e30ed01378ed", "001289a1-260c-466c-8def-5a786cf06ca7", "0012c0d0-6224-4f8a-84a6-0a4281bd8837", "0013519c-6753-4fe1-afff-22e0060140c7", "00135d25-b5f8-4bea-92ae-9bbecb2b441f", "0013f7e9-8def-45e0-aaf2-16cbc09d3d34", "0014d899-a29e-4472-84aa-e8b42ccaa687", "0015da03-c836-4e58-bfd7-d5bac17f8c3e", "0015e295-18a9-4bd2-ab44-99cf0a5cd4ee", "0016716f-e980-4aa7-b196-13bb9f69215a", "00193a18-dba5-43b

alanorth

#!/usr/bin/env python3

import re

import requests


# Enumerate the cores in Solr to determine if statistics have been sharded into
# yearly shards by DSpace's stats-util or not (for example: statistics-2018).
def get_statistics_shards():

alanorth

Software Installation Notes

A list of software installed on the Monster server in Addis in 2020-08:

• AdapterRemoval/2.3.1
• AdmixTools/7.0.1
• bamstats/1.25
• bcftools/1.10.2
• bowtie2/2.4.1
• fastq_screen/0.14.1
• fastqc/0.11.9

alanorth

{
  "3166-1": [
    {
      "alpha_2": "AW",
      "alpha_3": "ABW",
      "name": "Aruba",
      "numeric": "533"
    },
    {
      "alpha_2": "AF",

alanorth

import json

from org.dspace.core import ConfigurationManager
from org.dspace.curate import ScriptedTask


class MyTask(ScriptedTask):
    def init(self, curator, taskName):
        print "Initializing MyTask with Jython"