Mercurial > repos > ximgchess > chap_test_20230411
changeset 160:262b81603e4e draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit bd55c86b9f7bfabff0bbec1f10704850fec82f02-dirty
| author | ximgchess |
|---|---|
| date | Fri, 30 Jun 2023 13:34:19 +0000 |
| parents | b2e914633e61 |
| children | f524e7c848f6 |
| files | chapbook_demo/chapbook_demo.xml |
| diffstat | 1 files changed, 12 insertions(+), 3 deletions(-) [+] |
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--- a/chapbook_demo/chapbook_demo.xml Fri Jun 30 13:21:22 2023 +0000 +++ b/chapbook_demo/chapbook_demo.xml Fri Jun 30 13:34:19 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy6" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@"> +<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy7" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@"> <macros> <import>../macros.xml</import> </macros> @@ -9,11 +9,20 @@ <requirement type="package" version="1.10.7">pydantic</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + ## certif-pyspec is not available over any conda channels, so + ## pip install the package the first time this tool is run pip --exists-action i install certif-pyspec==1.5.3 && - indir=$(realpath ) - ln -s \$(realpath '$indir')/* '$__tool_directory__' && + ## Create symlinks in the tool directory to all items in the + ## input directory provided by the user + #import os.path + #set $norm_indir = os.path.normpath('$indir') + ln -s '$norm_indir'/* '$__tool_directory__' && + + ## Run the pipeline provided CHAP --config '$config' && + + ## Unlink the symlinks created previously find '$__tool_directory__' -type l -exec unlink {} \; ]]></command> <environment_variables>