Mercurial > repos > iuc > jbrowse
changeset 35:3235aeb45c22 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
| author | iuc |
|---|---|
| date | Wed, 18 Dec 2019 10:46:52 -0500 |
| parents | 9de82b4963e6 |
| children | 7ed0827da5a8 |
| files | jbrowse-fromdir.xml jbrowse.xml macros.xml |
| diffstat | 3 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/jbrowse-fromdir.xml Wed Sep 11 09:40:36 2019 -0400 +++ b/jbrowse-fromdir.xml Wed Dec 18 10:46:52 2019 -0500 @@ -7,12 +7,15 @@ <command detect_errors="exit_code"><![CDATA[ ## Create output directory mkdir -p $output.files_path && + +export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse && + ## Copy in jbrowse cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ && ## Copy in data directory cp -R $input.dataset.extra_files_path/data/ $output.files_path/ && -mv $output.files_path/index.html $output +cp $output.files_path/index.html $output ]]></command> <inputs> <param label="JBrowse Data Directory"
--- a/jbrowse.xml Wed Sep 11 09:40:36 2019 -0400 +++ b/jbrowse.xml Wed Dec 18 10:46:52 2019 -0500 @@ -16,6 +16,8 @@ ## but nice if users want to reproduce locally cp $trackxml $output.files_path/galaxy.xml && +export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse && + ## Once that's done, we run the python script to handle the real work python '$__tool_directory__/jbrowse.py' @@ -28,14 +30,14 @@ $trackxml && #if str($standalone) == "Complete": - mv $output.files_path/index.html $output; + cp $output.files_path/index.html $output; #else: - mv $dummyIndex $output; + cp $dummyIndex $output; #end if ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. #if str($uglyTestingHack) == "enabled": - mv $trackxml $output + cp $trackxml $output #end if ]]></command> <configfiles>
--- a/macros.xml Wed Sep 11 09:40:36 2019 -0400 +++ b/macros.xml Wed Dec 18 10:46:52 2019 -0500 @@ -14,7 +14,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">galaxy5</token> + <token name="@WRAPPER_VERSION@">galaxy6</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution**