| Previous changeset 2:f6bc74863c1c (2016-12-07) Next changeset 4:384b972e43bc (2017-08-01) |
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Commit message:
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty |
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modified:
je je-markdupes.xml macros.xml |
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added:
README.md je_1.1_bundle.jar |
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removed:
je_1.0_bundle.jar |
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| diff -r f6bc74863c1c -r 4ccf1406832d README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jun 21 05:23:33 2017 -0400 |
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| @@ -0,0 +1,19 @@ +# HowTo update the toolshed repository + +After linting/testing your update using ``planemo test`` and ``planemo serve`` you can upload the changes to the toolshed repos. + +For this you need to have the credentials or api_key of our ``gbcs-embl-heidelberg`` user. +To make it easier, put this information in your global ``~/.planemo.yml`` file. The format is described here: https://planemo.readthedocs.io/en/latest/configuration.html + +The commands below work due to the ``.shed.yml`` file in this directory. + +## Update testtoolshed + +``planemo shed_update --shed_target testtoolshed`` + +Look at the result and then update the main toolshed. + +## Update toolshed + +``planemo shed_update --shed_target toolshed`` + |
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| diff -r f6bc74863c1c -r 4ccf1406832d je --- a/je Wed Dec 07 11:57:09 2016 -0500 +++ b/je Wed Jun 21 05:23:33 2017 -0400 |
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| @@ -1,11 +1,11 @@ #!/bin/sh -# Wrapper around je_1.0_bundle.jar +# Wrapper around je_1.1_bundle.jar # where are we stored ? DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" # echo $DIR # path to jar file to execute, this jar is supposed to be in the same dir as this script -JAR_FILE=$DIR"/je_1.0_bundle.jar" +JAR_FILE=$DIR"/je_1.1_bundle.jar" # set default _JAVA_OPTIONS _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'} |
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| diff -r f6bc74863c1c -r 4ccf1406832d je-markdupes.xml --- a/je-markdupes.xml Wed Dec 07 11:57:09 2016 -0500 +++ b/je-markdupes.xml Wed Jun 21 05:23:33 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="je_markdupes" name="Je-MarkDuplicates" version="1.0"> +<tool id="je_markdupes" name="Je-MarkDuplicates" version="@VERSION_STRING@"> <description>to filter BAM files for read duplicates taking UMIs into account</description> <macros> <import>macros.xml</import> |
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| diff -r f6bc74863c1c -r 4ccf1406832d je_1.0_bundle.jar |
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| Binary file je_1.0_bundle.jar has changed |
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| diff -r f6bc74863c1c -r 4ccf1406832d je_1.1_bundle.jar |
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| Binary file je_1.1_bundle.jar has changed |
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| diff -r f6bc74863c1c -r 4ccf1406832d macros.xml --- a/macros.xml Wed Dec 07 11:57:09 2016 -0500 +++ b/macros.xml Wed Jun 21 05:23:33 2017 -0400 |
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| @@ -1,5 +1,7 @@ <macros> + <token name="@VERSION_STRING@">1.1</token> + <token name="@single_or_paired_cmd@"> #if str( $library.type ) == "single": F1=${library.input_1} |