Mercurial > repos > peterjc > venn_list
changeset 22:2a1025bbd637 draft
Tool Shed dependency for rpy and limma
| author | peterjc |
|---|---|
| date | Sat, 10 Oct 2015 08:48:45 -0400 |
| parents | 29d647a7dc39 |
| children | c4ec51cb5acc |
| files | tools/venn_list/README.rst tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.xml |
| diffstat | 3 files changed, 14 insertions(+), 5 deletions(-) [+] |
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--- a/tools/venn_list/README.rst Thu May 21 10:51:26 2015 -0400 +++ b/tools/venn_list/README.rst Sat Oct 10 08:48:45 2015 -0400 @@ -72,6 +72,7 @@ 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). ======= ====================================================================== @@ -88,12 +89,12 @@ 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):: - $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ ... or:: - $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ ... To just build and check the tar ball, use::
--- a/tools/venn_list/tool_dependencies.xml Thu May 21 10:51:26 2015 -0400 +++ b/tools/venn_list/tool_dependencies.xml Sat Oct 10 08:48:45 2015 -0400 @@ -1,5 +1,11 @@ <?xml version="1.0"?> <tool_dependency> + <package name="limma" version="3.25.3"> + <repository changeset_revision="55850b0ff6a3" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="rpy" version="1.0.3"> + <repository changeset_revision="c0eb80864491" name="package_rpy_1_0_3" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="biopython" version="1.65"> <repository changeset_revision="f8d72690eeae" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package>
--- a/tools/venn_list/venn_list.xml Thu May 21 10:51:26 2015 -0400 +++ b/tools/venn_list/venn_list.xml Sat Oct 10 08:48:45 2015 -0400 @@ -2,8 +2,10 @@ <description>from lists</description> <requirements> <requirement type="python-module">rpy</requirement> + <requirement type="python-module">Bio</requirement> + <requirement type="package" version="1.0.3">rpy</requirement> + <requirement type="package" version="3.25.3">limma</requirement> <requirement type="package" version="1.65">biopython</requirement> - <requirement type="python-module">Bio</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -71,7 +73,7 @@ <assert_stdout> <has_line line="Doing 3-way Venn Diagram" /> <has_line line="Inferred total of 10 IDs" /> - <has_line line="6 in Rhodopsins" /> + <has_line line="6 in Rhodopsins" /> <has_line line="4 in Human" /> <has_line line="1 in Human vs Rhodopsin BLAST" /> </assert_stdout> @@ -85,7 +87,7 @@ <param name="sets_1|set" value="four_human_proteins.fasta"/> <param name="sets_1|lab" value="Human"/> <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> - <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> + <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> <assert_stdout> <has_line line="Doing 3-way Venn Diagram" /> <has_line line="Total of 10 IDs" />