| Previous changeset 1:0af41de4eda1 (2016-06-07) Next changeset 3:847db7b39bdc (2016-12-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504 |
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modified:
snpSift_geneSets.xml snpSift_macros.xml |
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| diff -r 0af41de4eda1 -r 9ba6e2c298ab snpSift_geneSets.xml --- a/snpSift_geneSets.xml Tue Jun 07 10:05:20 2016 -0400 +++ b/snpSift_geneSets.xml Mon Sep 19 14:43:55 2016 -0400 |
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| @@ -10,6 +10,7 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ + @CONDA_SNPEFF_JAR_PATH@ && java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v #if $db_opts.db_opts_selector == "db" "${db_opts.database.fields.path}" |
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| diff -r 0af41de4eda1 -r 9ba6e2c298ab snpSift_macros.xml --- a/snpSift_macros.xml Tue Jun 07 10:05:20 2016 -0400 +++ b/snpSift_macros.xml Mon Sep 19 14:43:55 2016 -0400 |
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| @@ -10,8 +10,13 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> + <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token> <xml name="version_command"> - <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> + <version_command><![CDATA[ + if [ -z "$SNPEFF_JAR_PATH" ]; then + export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff))); + fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version + ]]></version_command> </xml> <token name="@WRAPPER_VERSION@">4.1</token> <token name="@EXTERNAL_DOCUMENTATION@"> |