Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/README.md @ 33:c5290ea7bae0 draft

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author fubar
date Sat, 08 Aug 2020 02:29:33 -0400
parents 4d578c8c1613
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32:4d578c8c1613 33:c5290ea7bae0
1 *WARNING before you start* 1 Note as at August 8 2020
2
3 Until a PR is accepted, galaxyxml requires a small tweak - you will need to install
4 ```
5 https://github.com/fubar2/galaxyxml
6 ```
7 instead into the virtualenv used to run galaxy and when using planemo, the
8
9 ```
10 --skip_venv
11 ```
12
13 flag must be used.
14
15
16 *WARNING before you start*
2 17
3 Install this tool on a private Galaxy ONLY 18 Install this tool on a private Galaxy ONLY
4 Please NEVER on a public or production instance 19 Please NEVER on a public or production instance
5 20
6 Updated august 2014 by John Chilton adding citation support 21 Updated august 2014 by John Chilton adding citation support
37 52
38 To use the ToolFactory, you should have prepared a script to paste into a 53 To use the ToolFactory, you should have prepared a script to paste into a
39 text box, or have a package in mind and a small test input example ready to select from your history 54 text box, or have a package in mind and a small test input example ready to select from your history
40 to test your new script. 55 to test your new script.
41 56
42 ```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me 57 ```planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/rossgit/toolfactory``` works for me
43 58
44 There is an example in each scripting language on the Tool Factory form. You 59 There is an example in each scripting language on the Tool Factory form. You
45 can just cut and paste these to try it out - remember to select the right 60 can just cut and paste these to try it out - remember to select the right
46 interpreter please. You'll also need to create a small test data set using 61 interpreter please. You'll also need to create a small test data set using
47 the Galaxy history add new data tool. 62 the Galaxy history add new data tool.
51 and execute again. Rinse, wash, repeat. 66 and execute again. Rinse, wash, repeat.
52 67
53 Once the script runs sucessfully, a new Galaxy tool that runs your script 68 Once the script runs sucessfully, a new Galaxy tool that runs your script
54 can be generated. Select the "generate" option and supply some help text and 69 can be generated. Select the "generate" option and supply some help text and
55 names. The new tool will be generated in the form of a new Galaxy datatype 70 names. The new tool will be generated in the form of a new Galaxy datatype
56 *toolshed.gz* - as the name suggests, it's an archive ready to upload to a 71 *tgz* - as the name suggests, it's an archive ready to upload to a
57 Galaxy ToolShed as a new tool repository. 72 Galaxy ToolShed as a new tool repository.
73
74 Until tgz is added to the galaxy distribution datatypes you will need to add the following:
75 <datatype extension="tgz" type="galaxy.datatypes.binary:Binary" subclass="true" mimetype="multipart/x-gzip" display_in_upload="true" />
76
77 to::
78 [galaxyroot]/config/datatypes_conf.xml
58 79
59 Once it's in a ToolShed, it can be installed into any local Galaxy server 80 Once it's in a ToolShed, it can be installed into any local Galaxy server
60 from the server administrative interface. 81 from the server administrative interface.
61 82
62 Once the new tool is installed, local users can run it - each time, the script 83 Once the new tool is installed, local users can run it - each time, the script