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  1.  
  2. Run conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830
  3. with:
  4. auto-update-conda: true
  5. conda-solver: libmamba
  6. conda-remove-defaults: true
  7. activate-environment: test
  8. auto-activate-base: true
  9. remove-profiles: true
  10. clean-patched-environment-file: true
  11. run-post: true
  12. env:
  13. GITHUB_TOKEN: ***
  14. NFT_VER: 0.9.2
  15. NFT_WORKDIR: ~
  16. NXF_ANSI_LOG: false
  17. NXF_SINGULARITY_CACHEDIR: /home/runner/work/metagenomeassembly/metagenomeassembly/.singularity
  18. NXF_SINGULARITY_LIBRARYDIR: /home/runner/work/metagenomeassembly/metagenomeassembly/.singularity
  19. TOTAL_SHARDS: 2
  20. JAVA_HOME: /opt/hostedtoolcache/Java_Zulu_jdk/17.0.16-8/x64
  21. JAVA_HOME_17_X64: /opt/hostedtoolcache/Java_Zulu_jdk/17.0.16-8/x64
  22. CAPSULE_LOG: none
  23. pythonLocation: /opt/hostedtoolcache/Python/3.13.7/x64
  24. PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.13.7/x64/lib/pkgconfig
  25. Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.7/x64
  26. Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.7/x64
  27. Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.7/x64
  28. LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.13.7/x64/lib
  29. NFT_DIFF:
  30. NFT_DIFF_ARGS:
  31. Gathering Inputs...
  32. Creating bootstrap condarc file in /home/runner/.condarc...
  33. Ensuring installer...
  34. Can we use bundled Miniconda?
  35. ... will use bundled Miniconda.
  36. Setup environment variables...
  37. Add "/usr/share/miniconda/condabin" to PATH
  38. Set 'CONDA="/usr/share/miniconda"'
  39. Parsing environment...
  40. Applying initial configuration...
  41. Removing implicitly added 'defaults' channel
  42. /usr/share/miniconda/condabin/conda config --remove channels defaults
  43. Adding pkgs_dir '/home/runner/conda_pkgs_dir'
  44. /usr/share/miniconda/condabin/conda config --add pkgs_dirs /home/runner/conda_pkgs_dir
  45. auto_activate_base: true
  46. /usr/share/miniconda/condabin/conda config --set auto_activate_base true
  47. Warning: WARNING conda.cli.main_config:_set_key(451): Key auto_activate_base is an alias of auto_activate; setting value with latter
  48.  
  49. WARNING conda.cli.main_config:_set_key(451): Key auto_activate_base is an alias of auto_activate; setting value with latter
  50. auto_update_conda: true
  51. /usr/share/miniconda/condabin/conda config --set auto_update_conda true
  52. solver: libmamba
  53. /usr/share/miniconda/condabin/conda config --set solver libmamba
  54. always_yes: true
  55. /usr/share/miniconda/condabin/conda config --set always_yes true
  56. changeps1: false
  57. /usr/share/miniconda/condabin/conda config --set changeps1 false
  58. /usr/share/miniconda/condabin/conda config --show-sources
  59. ==> /usr/share/miniconda/.condarc <==
  60. channels:
  61. - defaults
  62.  
  63. ==> /home/runner/.condarc <==
  64. auto_update_conda: True
  65. auto_activate: True
  66. notify_outdated_conda: False
  67. changeps1: False
  68. pkgs_dirs:
  69. - /home/runner/conda_pkgs_dir
  70. channels: []
  71. always_yes: True
  72. solver: libmamba
  73.  
  74. /usr/share/miniconda/condabin/conda config --show
  75. add_anaconda_token: True
  76. add_pip_as_python_dependency: True
  77. aggressive_update_packages:
  78. - ca-certificates
  79. - certifi
  80. - openssl
  81. allow_conda_downgrades: False
  82. allow_cycles: True
  83. allow_non_channel_urls: False
  84. allow_softlinks: False
  85. allowlist_channels: []
  86. always_copy: False
  87. always_softlink: False
  88. always_yes: True
  89. anaconda_anon_usage: True
  90. anaconda_heartbeat: False
  91. anaconda_upload: None
  92. auto_activate: True
  93. auto_stack: 0
  94. auto_update_conda: True
  95. bld_path:
  96. changeps1: False
  97. channel_alias: https://conda.anaconda.org
  98. channel_priority: flexible
  99. channel_settings: []
  100. channels:
  101. - defaults
  102. client_ssl_cert: None
  103. client_ssl_cert_key: None
  104. clobber: False
  105. conda_build: {}
  106. console: classic
  107. create_default_packages: []
  108. croot: /usr/share/miniconda/conda-bld
  109. custom_channels:
  110. pkgs/main: https://repo.anaconda.com
  111. pkgs/r: https://repo.anaconda.com
  112. pkgs/pro: https://repo.anaconda.com
  113. custom_multichannels:
  114. defaults:
  115. - https://repo.anaconda.com/pkgs/main
  116. - https://repo.anaconda.com/pkgs/r
  117. local:
  118. debug: False
  119. default_activation_env: base
  120. default_channels:
  121. - https://repo.anaconda.com/pkgs/main
  122. - https://repo.anaconda.com/pkgs/r
  123. default_python: 3.13
  124. default_threads: None
  125. denylist_channels: []
  126. deps_modifier: not_set
  127. dev: False
  128. disallowed_packages: []
  129. download_only: False
  130. dry_run: False
  131. enable_private_envs: False
  132. env_prompt: ({default_env})
  133. environment_specifier: None
  134. envs_dirs:
  135. - /usr/share/miniconda/envs
  136. - /home/runner/.conda/envs
  137. envvars_force_uppercase: True
  138. error_upload_url: https://conda.io/conda-post/unexpected-error
  139. execute_threads: 1
  140. experimental: []
  141. extra_safety_checks: False
  142. fetch_threads: 5
  143. force: False
  144. force_32bit: False
  145. force_reinstall: False
  146. force_remove: False
  147. ignore_pinned: False
  148. json: False
  149. list_fields:
  150. - name
  151. - version
  152. - build
  153. - channel_name
  154. local_repodata_ttl: 1
  155. migrated_channel_aliases: []
  156. migrated_custom_channels: {}
  157. no_lock: False
  158. no_plugins: False
  159. non_admin_enabled: True
  160. notify_outdated_conda: False
  161. number_channel_notices: 5
  162. offline: False
  163. override_channels_enabled: True
  164. path_conflict: clobber
  165. pinned_packages: []
  166. pkgs_dirs:
  167. - /home/runner/conda_pkgs_dir
  168. plugins:
  169. anaconda_telemetry: True
  170. auto_accept_tos: False
  171. prefix_data_interoperability: False
  172. protect_frozen_envs: True
  173. proxy_servers: {}
  174. quiet: False
  175. register_envs: True
  176. remote_backoff_factor: 1
  177. remote_connect_timeout_secs: 9.15
  178. remote_max_retries: 3
  179. remote_read_timeout_secs: 60.0
  180. repodata_fns:
  181. - current_repodata.json
  182. - repodata.json
  183. repodata_threads: None
  184. repodata_use_zst: True
  185. report_errors: None
  186. restore_free_channel: False
  187. rollback_enabled: True
  188. root_prefix: /usr/share/miniconda
  189. safety_checks: warn
  190. sat_solver: pycosat
  191. separate_format_cache: False
  192. shortcuts: True
  193. shortcuts_only: []
  194. show_channel_urls: None
  195. signing_metadata_url_base: None
  196. solver: libmamba
  197. solver_ignore_timestamps: False
  198. ssl_verify: True
  199. subdir: linux-64
  200. subdirs:
  201. - linux-64
  202. - noarch
  203. target_prefix_override:
  204. trace: False
  205. track_features: []
  206. unsatisfiable_hints: True
  207. unsatisfiable_hints_check_depth: 2
  208. update_modifier: update_specs
  209. use_index_cache: False
  210. use_local: False
  211. use_only_tar_bz2: None
  212. verbosity: 0
  213. verify_threads: 1
  214. Initializing conda shell integration...
  215. Removing "/home/runner/.bashrc"
  216. Removing "/home/runner/.bash_profile"
  217. Removing "/home/runner/.profile"
  218. /usr/share/miniconda/condabin/conda init --all
  219. no change /usr/share/miniconda/condabin/conda
  220. no change /usr/share/miniconda/bin/conda
  221. no change /usr/share/miniconda/bin/conda-env
  222. no change /usr/share/miniconda/bin/activate
  223. no change /usr/share/miniconda/bin/deactivate
  224. no change /usr/share/miniconda/etc/profile.d/conda.sh
  225. no change /usr/share/miniconda/etc/fish/conf.d/conda.fish
  226. no change /usr/share/miniconda/shell/condabin/Conda.psm1
  227. modified /usr/share/miniconda/shell/condabin/conda-hook.ps1
  228. no change /usr/share/miniconda/lib/python3.13/site-packages/xontrib/conda.xsh
  229. no change /usr/share/miniconda/etc/profile.d/conda.csh
  230. modified /home/runner/.bashrc
  231. modified /home/runner/.zshrc
  232. modified /home/runner/.config/fish/config.fish
  233. modified /home/runner/.xonshrc
  234. modified /home/runner/.tcshrc
  235.  
  236. ==> For changes to take effect, close and re-open your current shell. <==
  237.  
  238. Renaming "/home/runner/.bashrc" to "/home/runner/.profile"
  239.  
  240. Append to "/home/runner/.profile":
  241.  
  242. # ----------------------------------------------------------------------------
  243. # Conda Setup Action: Basic configuration
  244. set -eo pipefail
  245. # Conda Setup Action: Custom activation
  246. conda activate "test"
  247. # ----------------------------------------------------------------------------
  248.  
  249. Append to "/home/runner/.zshrc":
  250.  
  251. # ----------------------------------------------------------------------------
  252. # Conda Setup Action: Basic configuration
  253. set -eo pipefail
  254. # Conda Setup Action: Custom activation
  255. conda activate "test"
  256. # ----------------------------------------------------------------------------
  257.  
  258. Append to "/home/runner/.config/fish/config.fish":
  259.  
  260. # ----------------------------------------------------------------------------
  261. # Conda Setup Action: Basic configuration
  262. set -eo pipefail
  263. # Conda Setup Action: Custom activation
  264. conda activate "test"
  265. # ----------------------------------------------------------------------------
  266.  
  267. Append to "/home/runner/.tcshrc":
  268.  
  269. # ----------------------------------------------------------------------------
  270. # Conda Setup Action: Basic configuration
  271. set -eo pipefail
  272. # Conda Setup Action: Custom activation
  273. conda activate "test"
  274. # ----------------------------------------------------------------------------
  275.  
  276. Append to "/home/runner/.xonshrc":
  277.  
  278. # ----------------------------------------------------------------------------
  279. # Conda Setup Action: Basic configuration
  280. set -eo pipefail
  281. # Conda Setup Action: Custom activation
  282. conda activate "test"
  283. # ----------------------------------------------------------------------------
  284.  
  285. Adding tools to 'base' env...
  286. Do we need to update conda?
  287. Do we need to update mamba?
  288. Do we need to update python?
  289. Do we need to update conda-build?
  290. No tools were installed in 'base' env.
  291. No post-install actions were taken on 'base' env.
  292. Ensuring environment...
  293. Can we conda create (from explicit)?
  294. Can we conda create (simple)?
  295. ... will conda create (simple).
  296. Updating 'test' env from conda create (simple)...
  297. /usr/share/miniconda/condabin/conda create --name test
  298. CI detected...
  299. By accessing https://repo.anaconda.com/pkgs/main via CI for this repository you
  300. acknowledge and agree to the Terms of Service:
  301. ANACONDA TERMS OF SERVICE
  302. Effective Date: July 15, 2025
  303.  
  304. See https://anaconda.com/legal/terms/terms-of-service
  305. By accessing https://repo.anaconda.com/pkgs/r via CI for this repository you
  306. acknowledge and agree to the Terms of Service:
  307. ANACONDA TERMS OF SERVICE
  308. Effective Date: July 15, 2025
  309.  
  310. See https://anaconda.com/legal/terms/terms-of-service
  311. 2 channel Terms of Service accepted
  312. Retrieving notices: - done
  313. Channels:
  314. - defaults
  315. Platform: linux-64
  316. Collecting package metadata (repodata.json): | / - \ | / - done
  317. Solving environment: | done
  318.  
  319. ## Package Plan ##
  320.  
  321. environment location: /usr/share/miniconda/envs/test
  322.  
  323.  
  324.  
  325.  
  326. Downloading and Extracting Packages: ...working... done
  327. Preparing transaction: - done
  328. Verifying transaction: | done
  329. Executing transaction: - done
  330. #
  331. # To activate this environment, use
  332. #
  333. # $ conda activate test
  334. #
  335. # To deactivate an active environment, use
  336. #
  337. # $ conda deactivate
  338.  
  339.  
  340. setup-miniconda ran successfully
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