With the following channels:

$ guix describe
Generation 3    Aug 28 2025 03:56:44    (current)
  gn-bioinformatics cffafde
    repository URL: file:///home/bonfacem/guix-bioinformatics/
    branch: master
    commit: cffafde125f3e711418d3ebb62eacd48a3efa8cf
  guix-forge 3c8dc85
    repository URL: https://git.genenetwork.org/guix-forge/
    branch: main
    commit: 3c8dc85a584c98bc90088ec1c85933d4d10e7383
  guix-past b14d7f9
    repository URL: https://codeberg.org/guix-science/guix-past
    branch: master
    commit: b14d7f997ae8eec788a7c16a7252460cba3aaef8
  guix 34453b9
    repository URL: https://codeberg.org/guix/guix
    branch: master
    commit: 34453b97005ff86355399df89c8827c57839d9c7

Running:

$ guix shell -C genenetwork2

Produces:

guix shell: error: unshare: 268566528: Invalid argument
Backtrace:
          16 (primitive-load "/export3/local/home/bonfacem/.guix-ext…")
In guix/ui.scm:
   2399:7 15 (run-guix . _)
  2362:10 14 (run-guix-command _ . _)
In ice-9/boot-9.scm:
  1752:10 13 (with-exception-handler _ _ #:unwind? _ # _)
In guix/status.scm:
    842:4 12 (call-with-status-report _ _)
In guix/store.scm:
    703:3 11 (_)
In ice-9/boot-9.scm:
  1752:10 10 (with-exception-handler _ _ #:unwind? _ # _)
In guix/store.scm:
   690:37  9 (thunk)
   1331:8  8 (call-with-build-handler _ _)
   1331:8  7 (call-with-build-handler #<procedure 7fc86bb50de0 at g…> …)
In guix/scripts/environment.scm:
  1205:11  6 (proc _)
In guix/store.scm:
  2212:25  5 (run-with-store #<store-connection 256.100 7fc87a46d820> …)
In guix/scripts/environment.scm:
    911:8  4 (_ _)
In gnu/build/linux-container.scm:
    485:7  3 (call-with-container _ _ #:namespaces _ #:host-uids _ # …)
In unknown file:
           2 (waitpid #f #<undefined>)
In ice-9/boot-9.scm:
  1685:16  1 (raise-exception _ #:continuable? _)
  1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
Wrong type (expecting exact integer): #f

Still unable to work out what the issue with the shell is.

Stack trace:

2025-09-03 12:23:32 In ice-9/eval.scm:
2025-09-03 12:23:32    191:35  3 (_ #f)
2025-09-03 12:23:32 In gnu/build/linux-container.scm:
2025-09-03 12:23:32     368:8  2 (call-with-temporary-directory #<procedure 7f012241d3f0?>)
2025-09-03 12:23:32     485:7  1 (_ "/tmp/guix-directory.Bl6jtx")
2025-09-03 12:23:32 In unknown file:
2025-09-03 12:23:32            0 (waitpid #f #<undefined>)
2025-09-03 12:23:32

Cryptic message. Running the g-exps as a program shows:

Receiving objects: 100% (698/698), 16.18 MiB | 30.29 MiB/s, done.
Resolving deltas: 100% (49/49), done.
==================================================
error: cannot run less: No such file or directory
fatal: unable to execute pager 'less'
Backtrace:
           5 (primitive-load "/gnu/store/c9bvy90s5mglp6xdfkc1s4qkzj8?")
In ice-9/eval.scm:
    619:8  4 (_ #f)
In ice-9/boot-9.scm:
    142:2  3 (dynamic-wind #<procedure 7fa954b25880 at ice-9/eval.s?> ?)
    142:2  2 (dynamic-wind #<procedure 7fa94b7970c0 at ice-9/eval.s?> ?)
In ice-9/eval.scm:
    619:8  1 (_ #(#(#<directory (guile-user) 7fa954b03c80>)))
In guix/build/utils.scm:
    822:6  0 (invoke "git" "log" "--max-count" "1")

guix/build/utils.scm:822:6: In procedure invoke:
ERROR:
  1. &invoke-error:
      program: "git"
      arguments: ("log" "--max-count" "1")
      exit-status: 128
      term-signal: #f
      stop-signal: #f

Fixed by adding "less" to the with-packages form and setting:

(setenv "TERM" "xterm-256color")

Despite having all file perms correctly set with 0644, we see:

Traceback (most recent call last):
  File "/gnu/store/ag1m9bv22iwm3sq87xly35y138l6kzd7-profile/lib/python3.11/site-packages/flask/app.py", line 917, in full_dispatch_request
    rv = self.dispatch_request()
         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/gnu/store/ag1m9bv22iwm3sq87xly35y138l6kzd7-profile/lib/python3.11/site-packages/flask/app.py", line 902, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/views.py", line 102, in authorise
    return with_db_connection(__authorise__)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/db/sqlite3.py", line 63, in with_db_connection
    return func(conn)
           ^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/views.py", line 90, in __authorise__
    return server.create_authorization_response(request=request, grant_user=user)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gnu/store/ag1m9bv22iwm3sq87xly35y138l6kzd7-profile/lib/python3.11/site-packages/authlib/oauth2/rfc6749/authorization_server.py", line 297, in create_authorization_response
    args = grant.create_authorization_response(redirect_uri, grant_user)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/grants/authorisation_code_grant.py", line 31, in create_authorization_response
    response = super().create_authorization_response(
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gnu/store/ag1m9bv22iwm3sq87xly35y138l6kzd7-profile/lib/python3.11/site-packages/authlib/oauth2/rfc6749/grants/authorization_code.py", line 158, in create_authorization_response
    self.save_authorization_code(code, self.request)
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/grants/authorisation_code_grant.py", line 45, in save_authorization_code
    return __save_authorization_code__(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/grants/authorisation_code_grant.py", line 106, in __save_authorization_code__
    return with_db_connection(lambda conn: save_authorisation_code(conn, code))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/db/sqlite3.py", line 63, in with_db_connection
    return func(conn)
           ^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/grants/authorisation_code_grant.py", line 106, in <lambda>
    return with_db_connection(lambda conn: save_authorisation_code(conn, code))
                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/export/data/repositories/gn-auth/gn_auth/auth/authentication/oauth2/models/authorization_code.py", line 92, in save_authorisation_code
    cursor.execute(
sqlite3.OperationalError: unable to open database file

Fixed above by correctly mapping:

-                                                (source auth-db-path)
+                                                (source (dirname auth-db-path))

in the relevant g-exp, and making sure that the parent directory is set to #o775 (rwx for both user/group).