# HG changeset patch # User gbcs-embl-heidelberg # Date 1498036973 14400 # Node ID 01fdc6d10660fcdc60b4b738735bef7b75c32288 # Parent 1f8df7e3539354e2f028c2a5b8c033e9cbebecea planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty diff -r 1f8df7e35393 -r 01fdc6d10660 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jun 21 05:22:53 2017 -0400 @@ -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`` + diff -r 1f8df7e35393 -r 01fdc6d10660 je --- a/je Wed Dec 07 11:57:30 2016 -0500 +++ b/je Wed Jun 21 05:22:53 2017 -0400 @@ -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'} diff -r 1f8df7e35393 -r 01fdc6d10660 je-demultiplex-illu.xml --- a/je-demultiplex-illu.xml Wed Dec 07 11:57:30 2016 -0500 +++ b/je-demultiplex-illu.xml Wed Jun 21 05:22:53 2017 -0400 @@ -1,4 +1,4 @@ - + demultiplexes fastq files using Illumina Index file macros.xml diff -r 1f8df7e35393 -r 01fdc6d10660 je_1.0_bundle.jar Binary file je_1.0_bundle.jar has changed diff -r 1f8df7e35393 -r 01fdc6d10660 je_1.1_bundle.jar Binary file je_1.1_bundle.jar has changed diff -r 1f8df7e35393 -r 01fdc6d10660 macros.xml --- a/macros.xml Wed Dec 07 11:57:30 2016 -0500 +++ b/macros.xml Wed Jun 21 05:22:53 2017 -0400 @@ -1,5 +1,7 @@ + 1.1 + #if str( $library.type ) == "single": F1=${library.input_1}