alanorth

# CIS Benchmark Adjustments
# See: https://github.com/alanorth/securekickstarts
kernel.randomize_va_space = 2 
net.ipv4.ip_forward = 0 
net.ipv4.conf.all.send_redirects = 0 
net.ipv4.conf.default.send_redirects = 0 
net.ipv4.conf.all.accept_source_route = 0 
net.ipv4.conf.default.accept_source_route = 0 
net.ipv4.conf.all.accept_redirects = 0 
net.ipv4.conf.default.accept_redirects = 0 

alanorth

- name: Copy Tomcat config(s)
  template: src={{ item.src }} dest={{ item.dest }} mode={{ item.mode }} owner=root group=root
  with_items:
    - { src: 'tomcat/server.xml.j2', dest: '/etc/tomcat7/server.xml', mode: '0644' }
    - { src: 'tomcat/tomcat-users.xml.j2', dest: '/etc/tomcat7/tomcat-users.xml', mode: '0640' }
  notify:
    - restart tomcat7
  tags: tomcat

- name: Prepare Tomcat web application contexts

alanorth

Gogs.io on Ubuntu 14.04

Create the VM

Create a VM using virt-install and feed it a preseed.

$ sudo virt-install --name gogs --ram 1024 --vcpus=1,cpuset=3 --cpu host --disk path=/home/aorth/software/vms/gogs.qcow2,size=40,bus=virtio,format=qcow2 --bridge=br0 --os-variant ubuntusaucy --location http://ubuntu.mirror.ac.ke/ubuntu/dists/trusty/main/installer-amd64 --graphics vnc -x "auto=true priority=critical url=http://192.168.5.3/~aorth/preseed/gogs.cfg"

You will have to configure the network manually (you can't set the network configuration in the preseed when using a network-based preseed, apparently).

Add users

alanorth

#!/bin/bash
#SBATCH -p batch
#SBATCH -J beast
#SBATCH -n 4

module load beast/1.7.5

DATA_DIR=~/data/beast_runs/
XML=H5N1_HA_NR.xml

alanorth

#!/bin/env bash
#SBATCH -p batch
# will use 15 CPUs
#SBATCH -n 15
# will use 2-3 different nodes
#SBATCH --nodes=2-3
#SBATCH -J ray

module load ray/2.3.1

alanorth

Keybase proof

I hereby claim:

• I am alanorth on github.
• I am alanorth (https://keybase.io/alanorth) on keybase.
• I have a public key whose fingerprint is 8CB0 D0AC B5CD 81EC 209C 6CDF BD1A 0E09 C2F8 36C0

To claim this, I am signing this object:

alanorth

Update XMLUI themes for new DSpace 4.x code / assets

The current CGSpace XMLUI themes are based on XMLUI as it was around DSpace 1.7/1.8, but were slightly update to take advantage of DSpace 3.x features, code, etc. We need to check the contents of current CGSpace XMLUI themes against the latest DSpace 4.x Mirage for new code, assets, best practices, etc.

From a brief look at the code, it seems this could happen in two phases:

• Phase 1: static, unchanged assets like images and JavaScript which we can copy in verbatim
• Phase 2: customized layout / display code like CSS and XSL which we have to integrate manually

Phase 1

Image directories:

alanorth

DSpace 4.x REST API

Ok, so this is pretty cool. I played with it a bit more and found some useful tidbits. The documentation for the REST API lists the following endpoints:

• /communities
• /collections
• /items
• /bitstreams

But I found there is also /handle which is much easier to work with because you don't have to know the internal database ID of a given community / collection / item, etc... you can just work using the same IDs you're used to from the DSpace front end.

DSpace Test has the REST webapp running here: https://cgspace.cgiar.org/rest

alanorth

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=2, minlength=239, maxlength=260)

alanorth

Start: Fri Apr 10 07:47:56 2015
HOST: Alans-MBP                   Loss%   Snt   Last   Avg  Best  Wrst StDev
  1.|-- homeportal                 0.0%    10    2.2   2.5   1.8   4.9   0.8
  2.|-- 172-7-164-2.lightspeed.sn  0.0%    10   21.1  21.5  21.0  22.5   0.0
  3.|-- ???                       100.0    10    0.0   0.0   0.0   0.0   0.0
  4.|-- 12.83.70.181               0.0%    10   24.6  24.5  22.1  27.5   1.6
  5.|-- ggr2.la2ca.ip.att.net     10.0%    10   28.7  28.5  26.0  35.3   2.8
  6.|-- las-bb1-link.telia.net     0.0%    10   25.6  27.4  25.6  31.6   2.1
  7.|-- nyk-bb1-link.telia.net     0.0%    10  107.0 103.6 102.9 107.0   1.2
  8.|-- prs-bb3-link.telia.net     0.0%    10  186.5 187.8 186.4 193.6   2.0