shed_upload.rst

shed_upload command

This section is auto-generated from the help text for the planemo command shed_upload. This help message can be generated with planemo shed_upload --help.

Usage:

planemo shed_upload [OPTIONS] PROJECT

Help

Low-level command to upload tarballs.

Generally, shed_update should be used instead since it also updates both tool shed contents (via tar ball generation and upload) as well as metadata (to handle metadata changes in .shed.yml files).

% planemo shed_upload --tar_only  ~/
% tar -tzf shed_upload.tar.gz
test-data/blastdb.loc
...
tools/ncbi_blast_plus/tool_dependencies.xml
% tar -tzf shed_upload.tar.gz | wc -l
117

Options:

-r, --recursive              Recursively perform command for nested repository
                             directories.
--fail_fast                  If multiple repositories are specified and an
                             error occurs stop immediately instead of
                             processing remaining repositories.
--owner TEXT                 Tool Shed repository owner (username).
--name TEXT                  Tool Shed repository name (defaults to the
                             inferred tool directory name).
--shed_email TEXT            E-mail for Tool Shed auth (required unless
                             shed_key is specified).
--shed_key TEXT              API key for Tool Shed access. An API key is
                             required unless e-mail and password is specified.
                             This key can be specified with either --shed_key
                             or --shed_key_from_env.
--shed_key_from_env TEXT     Environment variable to read API key for Tool
                             Shed access from.
--shed_password TEXT         Password for Tool Shed auth (required unless
                             shed_key is specified).
-t, --shed_target TEXT       Tool Shed to target (this can be 'toolshed',
                             'testtoolshed', 'local' (alias for
                             http://localhost:9009/), an arbitrary url or
                             mappings defined ~/.planemo.yml.
-m, --message TEXT           Commit message for tool shed upload.
--force_repository_creation  If a repository cannot be found for the specified
                             user/repo name pair, then automatically create
                             the repository in the toolshed.
--check_diff                 Skip uploading if the shed_diff detects there
                             would be no 'difference' (only attributes
                             populated by the shed would be updated.)
--tar_only                   Produce tar file for upload but do not publish to
                             a tool shed.
--tar FILE                   Specify a pre-existing tar file instead of
                             automatically building one as part of this
                             command.
--help                       Show this message and exit.