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FileConverter
FileFilter
FileInfo
FileMerger
IDMerger
IDFileConverter
MapStatistics
SpectraMerger
TextExporter
MzTabExporter

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diff -r eb61b02da186 config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample	Sun Jan 11 21:43:13 2015 -0500
+++ b/config/datatypes_conf.xml.sample	Mon Jan 12 17:37:25 2015 +0100
@@ -140,6 +140,8 @@
     <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
     <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
     <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
+    <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+    <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
     <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>

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diff -r eb26a9648323 lib/galaxy/webapps/galaxy/api/tool_data.py
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py	Tue Feb 03 09:00:51 2015 -0500
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py	Tue Feb 03 16:52:38 2015 +0100
@@ -28,6 +28,19 @@
 
     @web.require_admin
     @expose_api
+    def reload( self, trans, id, **kwd ):
+        """
+        GET /api/tool_data/{id}/reload

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<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="samtools" version="0.1.19">
        <repository name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="bedtools" version="2.22">
        <repository name="package_bedtools_2_22" owner="iuc" prior_installation_required="True" />
    </package>

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#!/bin/sh

arch=x86_64
pkg=ucsc
version=v312
build_deps="libc6-dev zlib1g-dev libncurses5-dev libpng-dev unzip libmysqlclient-dev libssl-dev"
urls="
http://hgdownload.soe.ucsc.edu/admin/jksrc.${version}.zip
"

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• read release notes and look for possible breakage, security fixes, new features
• hg pull && hg update stable
• backup Galaxy database (pg_dump -U > )
• update Galaxy database if necessary (sh manage_db.sh upgrade)
• search conflicts and resolve (check hg status)
• merge config/galaxy.ini and config/galaxy.ini.sample
• merge config/datatypes_conf.xml and config/datatypes_conf.xml.sample
• in general all config files should be merged with the *.sample files - meld is a good graphical editor for this
• run migration scripts (e.g. sh ./scripts/migrate_tools/0011_tools.sh install_dependencies)
• Update all Tool Shed tools and install new useful ones (find new one on News Brief and release notes from the last month)

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import logging
import argparse

...

parser.add_argument('-v', '--verbose', action="count", help="Set verbose lever by specifying multiple -v values.")

...

logger = logging.StreamHandler()

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[main]

# Following options are ignored if using the Galaxy dynamic proxy but
# are useful if mapping a range of ports for environment consumption.
#apache_urls = False
#password_auth = False
#ssl = False

[docker]

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#!/usr/bin/env sh

if mount | grep ^glxdk1:/var/tmp/glxdk1; then
    echo "/var/tmp/glxdk1 already mounted."
else
    sshfs glxdk1:/var/tmp/glxdk1 /var/tmp/glxdk1
    echo 'Mounting ...'
fi

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The Intergalactic Utilities Commission was organising it's first hackathon with the aim to make more tools collection aware.

The IUC was available for two days in a Hangout to answers questions and to work together with the Galaxy community to enhance our tools and the overall Galaxy ecosystem. Scientiests from three different continents participated in this and made it a very nice experience and a success story, which the IUC would like to repeat more often.

In the following a list of contributions: