Mercurial > repos > fubar > tool_factory_2
changeset 33:c5290ea7bae0 draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 08 Aug 2020 02:29:33 -0400 |
| parents | 4d578c8c1613 |
| children | 5052ac89c036 |
| files | toolfactory/README.md |
| diffstat | 1 files changed, 24 insertions(+), 3 deletions(-) [+] |
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--- a/toolfactory/README.md Fri Aug 07 23:14:54 2020 -0400 +++ b/toolfactory/README.md Sat Aug 08 02:29:33 2020 -0400 @@ -1,4 +1,19 @@ -*WARNING before you start* +Note as at August 8 2020 + +Until a PR is accepted, galaxyxml requires a small tweak - you will need to install +``` +https://github.com/fubar2/galaxyxml +``` +instead into the virtualenv used to run galaxy and when using planemo, the + +``` +--skip_venv +``` + +flag must be used. + + +*WARNING before you start* Install this tool on a private Galaxy ONLY Please NEVER on a public or production instance @@ -39,7 +54,7 @@ text box, or have a package in mind and a small test input example ready to select from your history to test your new script. -```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me +```planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/rossgit/toolfactory``` works for me There is an example in each scripting language on the Tool Factory form. You can just cut and paste these to try it out - remember to select the right @@ -53,9 +68,15 @@ Once the script runs sucessfully, a new Galaxy tool that runs your script can be generated. Select the "generate" option and supply some help text and names. The new tool will be generated in the form of a new Galaxy datatype -*toolshed.gz* - as the name suggests, it's an archive ready to upload to a +*tgz* - as the name suggests, it's an archive ready to upload to a Galaxy ToolShed as a new tool repository. +Until tgz is added to the galaxy distribution datatypes you will need to add the following: + <datatype extension="tgz" type="galaxy.datatypes.binary:Binary" subclass="true" mimetype="multipart/x-gzip" display_in_upload="true" /> + +to:: + [galaxyroot]/config/datatypes_conf.xml + Once it's in a ToolShed, it can be installed into any local Galaxy server from the server administrative interface.