Logs working

[agdiaz]

Add metadata context in YAML format :

schema_version: "1.0"
application:
  name: "scop3p-toolkit"
  title: "Scop3P-Toolkit"
  description: "Tools for exploring and extending Scop3P"
session:
  started_at_utc: "2026-05-20T12:53:55.458651+00:00"
  working_directory: "./galaxy_latest/database/jobs_directory/000/40/working"
  log_directory: "/var/log/scop3p_toolkit"
  log_file: "/var/log/scop3p_toolkit/scop3p_toolkit_log_20260520_125355_458896.log"
image:
  title: "Scop3P-Toolkit"
  version: "dev"
  revision: ""
  created: ""
  source: "https://github.com/Bio2Byte/Scop3P-notebooks"
  license: "Apache-2.0"
runtime:
  python: "3.12.13"
  python_implementation: "CPython"
  platform: "Linux-6.12.76-linuxkit-x86_64-with-glibc2.41"
  machine: "x86_64"
dependencies:
  shiny: "1.6.1"
  pandas: "2.2.3"
  requests: "2.33.1"
  numpy: "1.26.4"
  scipy: "1.12.0"
  networkx: "3.6.1"
  biopython: "1.87"
  py3Dmol: "2.5.4"
  pyvis: "0.3.2"
  bokeh: "3.9.0"
  b2bTools: "3.0.8"
  scop3p: "1.1.0"
external_tools:
  TM-align:
    path: "/usr/local/bin/TM-align"
    version: "**********************************************************************"
  hmmer:
    path: "/usr/bin/hmmsearch"
    version: "# hmmsearch :: search profile(s) against a sequence database"
  t_coffee:
    path: "/usr/bin/t_coffee"
    version: "PROGRAM: T-COFFEE Version_13.41.0.28bdc39 (2019-11-30 10:21:53 - Revision 5d5a1c1 - Build 465)"