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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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#!/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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[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]