claczny

I wanted to install Singularity on my M1 Pro (Ventura 13.1). As this chip is arm64 based, it turned out rather tricky. Some resources that I consulted although none of them presented a self-contained solution are below. I hadn't tried the solution via UTM as I had access to a Parallels Desktop license and did not necessarily want to have yet-another-tool installed.

• Instructions from Singularity itself: https://docs.sylabs.io/guides/3.0/user-guide/installation.html#install-on-windows-or-mac
• Video using UTM: https://www.youtube.com/watch?v=aKHbaytlS00
• https://github.com/manuparra/singularitycontainers-on-m1-arm64
• Another set of general instructions.: https://github.com/sPHENIX-Collaboration/Singularity/blob/master/OSX_installationguide.md

thanhleviet

- hosts: all
  become: true
  become_user: root
  vars:
    singularity_version: 3.10.0
  pre_tasks:
    - name: Update apt packages
      apt:
        update_cache: true
        cache_valid_time: 86400 #One day

natefoo

Running Galaxy on Kubernetes

Galaxy Community Conference 2019, Freiburg, Germany

This page: http://gxy.io/gcc19k8s/

Links

• Slides
• VM Spreadsheet
• Exercise 1: Galaxy Installation on Kubernetes

mohanpedala

Table of Contents

• set -e, -u, -x, -o pipefail
• set -e
• set -x
• set -u
• set -o pipefail
• Setting IFS
• Original Reference

set -e, -u, -x, -o pipefail

aksakalli

- name: Install Conda
  block:
    - name: Download Miniconda
      get_url:
        url: https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
        dest: /tmp/install-miniconda.sh
        checksum: md5:a946ea1d0c4a642ddf0c3a26a18bb16d
        mode: 0550
    - name: Create conda folder

hkwi

libvirt + prometheus + grafana

KVM を libvirt でホストしていて、prometheus と grafana で観測したい場合。 exporter の実装は 3 種類みつかる。流儀が異なり、メトリクスが異なるので注意。

• libvirt_exporter (Go)
  • grafana json + prometheus recording rule
  • prometheus の設定ファイルで recording rule を有効化します。
  • job 名は libvirt_exporter

hygull

STEPS

• Click on Help menu

• Select Enter License

• Then paste given KEY given at bottom

• Finally click on Use License

zacharycarter

Binding to C Libraries with Nim

---

Table of Contents

• Introduction
• C2Nim
• The C Preprocessor
• Pragmas

nsoranzo

If a handler log is full of messages like:

Workflow step 1585 of invocation 554 delayed

then probably a workflow invocation is stuck because a step was cancelled by a user. After verifying that this is the case, to stop the workflow invocation scheduling connect to the Galaxy database using psql and do the following:

galaxy_db=> SELECT * FROM workflow_invocation WHERE id=554;
 id  |        create_time         |        update_time         | workflow_id | history_id | state | scheduler | handler  |               uuid               
-----+----------------------------+----------------------------+-------------+------------+-------+-----------+----------+----------------------------------
 554 | 2016-11-16 17:24:38.586902 | 2016-11-16 17:26:34.555872 |         201 |        485 | ready | core      | handler1 | 8d49678eac2111e697b90050569af9e3

darogan

#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
# 
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
# 
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
#