eafgan
I hereby claim:
- I am afgane on github.
- I am eafgan (https://keybase.io/eafgan) on keybase.
- I have a public key ASBCgJ-Efu5HY_usIkS777EBXOwmJegBKD1nbaHH26HKZgo
To claim this, I am signing this object:
Enis Afgan afgane
afgane
/ galaxy-debug-pod.yml
Created
January 16, 2025 16:24
A manifest for a debug pod for a Galaxy deployment.
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| apiVersion: v1 | |
| kind: Pod | |
| metadata: | |
| name: gxy-debug-pod | |
| spec: | |
| containers: | |
| - name: gxy-debug-pod | |
| image: alpine:3.16 | |
| imagePullPolicy: IfNotPresent | |
| command: ["tail"] |
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| https://zenodo.org/record/4477881/files/X_test.tsv | |
| https://zenodo.org/record/4477881/files/X_train.tsv | |
| https://zenodo.org/record/4477881/files/y_test.tsv | |
| https://zenodo.org/record/4477881/files/y_train.tsv |
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| destinations: | |
| k8s: | |
| max_accepted_cores: 100 | |
| max_accepted_mem: 800 | |
| max_cores: 8 | |
| max_mem: 48 |
afgane
/ Build bonito container
Last active
November 2, 2020 02:45
Add AWS GPU instance to a K8s cluster. Tested with instance type g3 on Ubuntu 20.04.
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| docker run --gpus all -it nvidia/cuda:10.2-devel-ubuntu18.04 /bin/bash | |
| apt update && apt install -y python3 build-essential python3-pip libz-dev wget libncurses5 libncurses5-dev libbz2-dev liblzma-dev liblzma5 | |
| wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 | |
| tar -xf samtools-1.11.tar.bz2 | |
| cd samtools-1.11 | |
| ./configure --prefix /usr/local/ | |
| make | |
| make install | |
| pip3 install ont-bonito cupy-cuda102 |
afgane
/ playbook.yaml
Last active
October 13, 2020 03:53
A bare-bones Ansible playbook for (re)setting a new password for Rancher Admin user.
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| - name: Go | |
| hosts: all | |
| gather_facts: no | |
| vars: | |
| rancher_hostname: rancher.local | |
| pwd: pwd-from-cloudlaunch | |
| tasks: | |
| - name: Reset admin pwd | |
| # kubeconfig on k3s at /etc/rancher/k3s/k3s.yaml |
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| -- | |
| -- PostgreSQL database dump | |
| -- | |
| -- Dumped from database version 11.3 (Debian 11.3-1.pgdg90+1) | |
| -- Dumped by pg_dump version 11.3 (Debian 11.3-1.pgdg90+1) | |
| SET statement_timeout = 0; | |
| SET lock_timeout = 0; | |
| SET idle_in_transaction_session_timeout = 0; |
afgane
/ galaxy.log
Last active
August 6, 2019 15:55
Galaxy startup log, using `uwsgi --yaml config/galaxy.yml`
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| [uWSGI] getting YAML configuration from /galaxy/server/config/galaxy.yml | |
| [uwsgi-static] added mapping for /static/style => /galaxy/server/static/style/blue | |
| [uwsgi-static] added mapping for /static => /galaxy/server/static | |
| [uwsgi-static] added mapping for /favicon.ico => /galaxy/server/static/favicon.ico | |
| *** Starting uWSGI 2.0.18 (64bit) on [Tue Aug 6 15:04:56 2019] *** | |
| compiled with version: 4.8.2 20140120 (Red Hat 4.8.2-15) on 13 February 2019 12:48:51 | |
| os: Linux-4.4.0-1057-aws #66-Ubuntu SMP Thu May 3 12:49:47 UTC 2018 | |
| nodename: quelling-rodent-galaxy-web-545fbdf875-9w9wp | |
| machine: x86_64 | |
| clock source: unix |
afgane
/ cl
Created
July 7, 2019 16:21
Launch a Ubuntu instance using the CLI via https://launch.usegalaxy.org
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| cloudlaunch deployments create --config-app ubuntu_launch_data.json "instance-name" ubuntu aws 11 --application-version "16.04 (with Docker)" |
afgane
/ cl
Created
July 7, 2019 16:21
Launch a Ubuntu instance using the CLI via https://launch.usegalaxy.org
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| cloudlaunch deployments create --config-app ubuntu_launch_data.json "instance-name" ubuntu aws 11 --application-version "16.04 (with Docker)" |
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