Mercurial > repos > peterjc > venn_list
diff tools/venn_list/README.rst @ 5:26e35d5133a1 draft
v0.0.9 - Tool Shed dependency for rpy and limma
author | peterjc |
---|---|
date | Sat, 10 Oct 2015 08:52:01 -0400 |
parents | 991342eca214 |
children | ea68a1a4c1d9 |
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--- a/tools/venn_list/README.rst Wed Apr 29 11:00:41 2015 -0400 +++ b/tools/venn_list/README.rst Sat Oct 10 08:52:01 2015 -0400 @@ -18,9 +18,8 @@ ====================== This should be straightforward, Galaxy should automatically download the tool -and the Biopython dependency. - -You will still need to install the R/Bioconductor package limma. +and the Python dependencies Biopython and rpy, and the R/Bioconductor package +limma. Manual Installation @@ -69,6 +68,10 @@ - Fixed and improved error handling when rpy is not available. - Test output relaxed to cope with more variation in PDF output. - Declare Biopython dependency via the Tool Shed. +v0.0.9 - Test with three-way Venn diagram. + - Includes testing of failure mode. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Tool Shed dependency for rpy and limma (thanks to Björn Grüning). ======= ====================================================================== @@ -81,21 +84,30 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + ... + +or:: -Check this worked:: + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + ... + +To just build and check the tar ball, use:: - $ tar -tzf venn_list.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ + ... + $ tar -tzf shed_upload.tar.gz tools/venn_list/README.rst + tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.py tools/venn_list/venn_list.xml - tools/venn_list/tool_dependencies.xml test-data/magic.pdf + test-data/rhodopsin_proteins.fasta test-data/venn_list.tabular - test-data/rhodopsin_proteins.fasta Licence (MIT)