[med-svn] r16470 - in trunk/packages/galaxy/trunk/debian: . patches
Timothy Booth
tbooth-guest at moszumanska.debian.org
Tue Mar 18 17:33:58 UTC 2014
Author: tbooth-guest
Date: 2014-03-18 17:33:58 +0000 (Tue, 18 Mar 2014)
New Revision: 16470
Removed:
trunk/packages/galaxy/trunk/debian/patches/authenticate_via_pam
trunk/packages/galaxy/trunk/debian/patches/clustalw_not_clustalw2
trunk/packages/galaxy/trunk/debian/patches/misc_configuration_tweaks
trunk/packages/galaxy/trunk/debian/patches/samtools_use_deb_package
trunk/packages/galaxy/trunk/debian/universe_wsgi.ini.hacked
Modified:
trunk/packages/galaxy/trunk/debian/rules
Log:
Remove some cruft now I have it squirreled in SVN
Deleted: trunk/packages/galaxy/trunk/debian/patches/authenticate_via_pam
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/authenticate_via_pam 2014-03-18 17:22:19 UTC (rev 16469)
+++ trunk/packages/galaxy/trunk/debian/patches/authenticate_via_pam 2014-03-18 17:33:58 UTC (rev 16470)
@@ -1,24 +0,0 @@
---- a/lib/galaxy/model/__init__.py
-+++ b/lib/galaxy/model/__init__.py
-@@ -97,6 +97,11 @@
- """
- Check if `cleartext` matches user password when hashed.
- """
-+ if self.password == 'PAM':
-+ #TODO - check cleartext by calling to validator service
-+ if cleartext = 'password':
-+ return True
-+
- return galaxy.security.passwords.check_password( cleartext, self.password )
-
- def all_roles( self ):
---- a/lib/galaxy/webapps/galaxy/controllers/user.py
-+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
-@@ -474,6 +474,7 @@
- success = False
- user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first()
- if not user:
-+ #TODO - if system logins are allowed, see about auto-adding the user
- message = "No such user (please note that login is case sensitive)"
- status = 'error'
- elif user.deleted:
Deleted: trunk/packages/galaxy/trunk/debian/patches/clustalw_not_clustalw2
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/clustalw_not_clustalw2 2014-03-18 17:22:19 UTC (rev 16469)
+++ trunk/packages/galaxy/trunk/debian/patches/clustalw_not_clustalw2 2014-03-18 17:33:58 UTC (rev 16470)
@@ -1,11 +0,0 @@
---- a/tools/rgenetics/rgClustalw.py
-+++ b/tools/rgenetics/rgClustalw.py
-@@ -18,7 +18,7 @@
-
- def run(self):
- tlf = open(self.opts.outlog,'w')
-- cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s -OUTPUT=%s' % (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts.outform)]
-+ cl = ['clustalw -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s -OUTPUT=%s' % (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts.outform)]
- if self.opts.seq_range_end <> None and self.opts.seq_range_start <> None:
- cl.append('-RANGE=%s,%s' % (self.opts.seq_range_start,self.opts.seq_range_end))
- if self.opts.outform=='CLUSTAL' and self.opts.outseqnos <> None:
Deleted: trunk/packages/galaxy/trunk/debian/patches/misc_configuration_tweaks
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/misc_configuration_tweaks 2014-03-18 17:22:19 UTC (rev 16469)
+++ trunk/packages/galaxy/trunk/debian/patches/misc_configuration_tweaks 2014-03-18 17:33:58 UTC (rev 16470)
@@ -1,52 +0,0 @@
-Simon suggested some more appropriate default configurations for a standalone
-server - see +bug/1064920
-Also I want to make it easy for people to proxy Galaxy through Apache and
-it doesn't seem to hurt to activate proxy-prefix by defualt.
---- a/universe_wsgi.ini.sample
-+++ b/universe_wsgi.ini.sample
-@@ -78,13 +78,14 @@
- # If running behind a proxy server and Galaxy is served from a subdirectory,
- # enable the proxy-prefix filter and set the prefix in the
- # [filter:proxy-prefix] section above.
--#filter-with = proxy-prefix
-+filter-with = proxy-prefix
-
- # If proxy-prefix is enabled and you're running more than one Galaxy instance
- # behind one hostname, you will want to set this to the same path as the prefix
- # in the filter above. This value becomes the "path" attribute set in the
- # cookie so the cookies from each instance will not clobber each other.
--#cookie_path = None
-+# Note - DO NOT include any / in this path
-+cookie_path = galaxy
-
- # -- Database
-
-@@ -439,7 +440,9 @@
- # added to a library. Set to True to enable. Please note the security
- # implication that this will give Galaxy Admins access to anything your Galaxy
- # user has access to.
--#allow_library_path_paste = False
-+# This should be fine on BL as Galaxy has an unprivileged account, and I'd assume
-+# that anyone having Galaxy admin access also has some shell access.
-+allow_library_path_paste = True
-
- # Users may choose to download multiple files from a library in an archive. By
- # default, Galaxy allows users to select from a few different archive formats
-@@ -506,7 +509,7 @@
- #allow_user_creation = True
-
- # Allow administrators to delete accounts.
--#allow_user_deletion = False
-+allow_user_deletion = True
-
- # Allow administrators to log in as other users (useful for debugging)
- #allow_user_impersonation = False
-@@ -514,7 +517,7 @@
- # Allow users to remove their datasets from disk immediately (otherwise,
- # datasets will be removed after a time period specified by an administrator in
- # the cleanup scripts run via cron)
--#allow_user_dataset_purge = False
-+allow_user_dataset_purge = True
-
- # By default, users' data will be public, but setting this to True will cause
- # it to be private. Does not affect existing users and data, only ones created
Deleted: trunk/packages/galaxy/trunk/debian/patches/samtools_use_deb_package
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/samtools_use_deb_package 2014-03-18 17:22:19 UTC (rev 16469)
+++ trunk/packages/galaxy/trunk/debian/patches/samtools_use_deb_package 2014-03-18 17:33:58 UTC (rev 16470)
@@ -1,11 +0,0 @@
---- a/tools/samtools/sam_merge.xml
-+++ b/tools/samtools/sam_merge.xml
-@@ -4,7 +4,7 @@
- <requirement type="package">picard</requirement>
- </requirements>
- <command>
--java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
-+/usr/bin/picard-tools MergeSamFiles MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
- #for $i in $inputs
- I=${i.input}
- #end for
Modified: trunk/packages/galaxy/trunk/debian/rules
===================================================================
--- trunk/packages/galaxy/trunk/debian/rules 2014-03-18 17:22:19 UTC (rev 16469)
+++ trunk/packages/galaxy/trunk/debian/rules 2014-03-18 17:33:58 UTC (rev 16470)
@@ -28,22 +28,10 @@
rm -f hacky_first_run.log
rm -rf database/tmp
rm -f lib/galaxy/datatypes/test/temp.txt
- #debian/link_configs_for_hacky_first_run.sh clean
#./debian/remove_obsolete_eggs.sh
override_dh_auto_build:
chmod a-x tool-data/*.loc.sample
- # The following is no longer needed but may yet be useful as it results in
- # a package that starts faster first time. On the other hand it also results
- # in a package that overwrites the database on updates, which is very much a bad
- # thing. Leaving it in in case I need to resurrect it.
- #debian/link_configs_for_hacky_first_run.sh
- #bash -c '( echo $$BASHPID ; python ./scripts/paster.py serve debian/universe_wsgi.ini.hacked 2>&1 ) \
- # | tee `tty -s && tty` ./hacky_first_run.log \
- # | ( SS=`head -n 1` ; grep -ql ^socket.gaierror && kill -TERM `ps -o pid --ppid $$SS --no-headers` )'
- #This needs to move as it is written to by the server
- #touch database/integrated_tool_panel.xml
- #debian/link_configs_for_hacky_first_run.sh clean
# Custom manual install to debian/tmp. Sorry - long winded.
override_dh_auto_install:
@@ -69,9 +57,6 @@
mkdir -p debian/tmp/usr/lib/galaxy-server/tool-data/shared/jars
#And some permissions fixes
find -type f -name '*.xml' -exec chmod a-x '{}' ';'
- #And scrub out build-time files from static/style
- # ( cd debian/tmp/usr/share/galaxy-server/static/style ; \
- # rm -rf *.tmpl *.less *.ini Makefile *.py bootstrap fontawesome shared_images )
( cd debian/tmp/usr/share/galaxy-server/static && \
rm june_2007_style && mkdir june_2007_style && mv style/blue june_2007_style && \
rm -r style )
Deleted: trunk/packages/galaxy/trunk/debian/universe_wsgi.ini.hacked
===================================================================
--- trunk/packages/galaxy/trunk/debian/universe_wsgi.ini.hacked 2014-03-18 17:22:19 UTC (rev 16469)
+++ trunk/packages/galaxy/trunk/debian/universe_wsgi.ini.hacked 2014-03-18 17:33:58 UTC (rev 16470)
@@ -1,681 +0,0 @@
-#
-# Galaxy is configured by default to be useable in a single-user development
-# environment. To tune the application for a multi-user production
-# environment, see the documentation at:
-#
-# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
-#
-
-# Throughout this sample configuration file, except where stated otherwise,
-# uncommented values override the default if left unset, whereas commented
-# values are set to the default value.
-# Examples of many of these options are explained in more detail in the wiki:
-#
-# http://wiki.g2.bx.psu.edu/Admin/Config
-#
-# Config hackers are encouraged to check there before asking for help.
-
-# ---- HTTP Server ----------------------------------------------------------
-
-# Configuration of the internal HTTP server.
-
-[server:main]
-
-# The internal HTTP server to use. Currently only Paste is provided. This
-# option is required.
-use = egg:Paste#http
-
-# The port on which to listen.
-port = -1
-
-# The address on which to listen. By default, only listen to localhost (Galaxy
-# will not be accessible over the network). Use '0.0.0.0' to listen on all
-# available network interfaces.
-host = 999.999.999.999
-
-# Use a threadpool for the web server instead of creating a thread for each
-# request.
-use_threadpool = False
-
-# Number of threads in the web server thread pool.
-#threadpool_workers = 10
-
-# ---- Filters --------------------------------------------------------------
-
-# Filters sit between Galaxy and the HTTP server.
-
-# These filters are disabled by default. They can be enabled with
-# 'filter-with' in the [app:main] section below.
-
-# Define the gzip filter.
-[filter:gzip]
-use = egg:Paste#xxx
-
-# Define the proxy-prefix filter.
-[filter:proxy-prefix]
-use = egg:PasteDeploy#prefix
-prefix = /galaxy
-
-# ---- Galaxy ---------------------------------------------------------------
-
-# Configuration of the Galaxy application.
-
-[app:main]
-
-# -- Application and filtering
-
-# The factory for the WSGI application. This should not be changed.
-paste.app_factory = galaxy.web.buildapp:app_factory
-
-# If not running behind a proxy server, you may want to enable gzip compression
-# to decrease the size of data transferred over the network. If using a proxy
-# server, please enable gzip compression there instead.
-#filter-with = gzip
-
-# If running behind a proxy server and Galaxy is served from a subdirectory,
-# enable the proxy-prefix filter and set the prefix in the
-# [filter:proxy-prefix] section above.
-#filter-with = proxy-prefix
-
-# If proxy-prefix is enabled and you're running more than one Galaxy instance
-# behind one hostname, you will want to set this to the same path as the prefix
-# in the filter above. This value becomes the "path" attribute set in the
-# cookie so the cookies from each instance will not clobber each other.
-#cookie_path = None
-
-# -- Database
-
-# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You
-# may use a SQLAlchemy connection string to specify an external database
-# instead. This string takes many options which are explained in detail in the
-# config file documentation.
-#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
-
-# If the server logs errors about not having enough database pool connections,
-# you will want to increase these values, or consider running more Galaxy
-# processes.
-#database_engine_option_pool_size = 5
-#database_engine_option_max_overflow = 10
-
-# If using MySQL and the server logs the error "MySQL server has gone away",
-# you will want to set this to some positive value (7200 should work).
-#database_engine_option_pool_recycle = -1
-
-# If large database query results are causing memory or response time issues in
-# the Galaxy process, leave the result on the server instead. This option is
-# only available for PostgreSQL and is highly recommended.
-#database_engine_option_server_side_cursors = False
-
-# Create only one connection to the database per thread, to reduce the
-# connection overhead. Recommended when not using SQLite:
-#database_engine_option_strategy = threadlocal
-
-# Log all database transactions, can be useful for debugging and performance
-# profiling. Logging is done via Python's 'logging' module under the qualname
-# 'galaxy.model.orm.logging_connection_proxy'
-#database_query_profiling_proxy = False
-
-# -- Files and directories
-
-# Dataset files are stored in this directory.
-#file_path = database/files
-
-# Temporary files are stored in this directory.
-#new_file_path = database/tmp
-
-# Tool config files, defines what tools are available in Galaxy.
-# Tools can be locally developed or installed from Galaxy tool sheds.
-#tool_config_file = tool_conf.xml,shed_tool_conf.xml
-
-# Default path to the directory containing the tools defined in tool_conf.xml.
-# Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
-#tool_path = tools
-
-# Path to the directory in which managed tool dependencies are placed. To use
-# the dependency system, see the documentation at:
-# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
-#tool_dependency_dir = None
-
-# Enable automatic polling of relative tool sheds to see if any updates
-# are available for installed repositories. Ideally only one Galaxy
-# server process should be able to check for repository updates. The
-# setting for hours_between_check should be an integer between 1 and 24.
-#enable_tool_shed_check = False
-#hours_between_check = 12
-
-# Directory where data used by tools is located, see the samples in that
-# directory and the wiki for help:
-# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
-#tool_data_path = tool-data
-
-# Directory where chrom len files are kept, currently mainly used by trackster
-#len_file_path = tool-data/shared/ucsc/chrom
-
-
-# Datatypes config file, defines what data (file) types are available in
-# Galaxy.
-#datatypes_config_file = datatypes_conf.xml
-
-# Each job is given a unique empty directory as its current working directory.
-# This option defines in what parent directory those directories will be
-# created.
-#job_working_directory = database/job_working_directory
-
-# If using a cluster, Galaxy will write job scripts and stdout/stderr to this
-# directory.
-#cluster_files_directory = database/pbs
-
-# External service types config file, defines what types of external_services configurations
-# are available in Galaxy.
-#external_service_type_config_file = external_service_types_conf.xml
-
-# Path to the directory containing the external_service_types defined in the config.
-#external_service_type_path = external_service_types
-
-# -- Mail and notification
-
-# Galaxy sends mail for various things: Subscribing users to the mailing list
-# if they request it, emailing password resets, notification from the Galaxy
-# Sample Tracking system, and reporting dataset errors. To do this, it needs
-# to send mail through an SMTP server, which you may define here (host:port).
-# Galaxy will automatically try STARTTLS but will continue upon failure.
-#smtp_server = None
-
-# If your SMTP server requires a username and password, you can provide them
-# here (password in cleartext here, but if your server supports STARTTLS it
-# will be sent over the network encrypted).
-#smtp_username = None
-#smtp_password = None
-
-# On the user registration form, users may choose to join the mailing list.
-# This is the address of the list they'll be subscribed to.
-#mailing_join_addr = galaxy-announce-join at bx.psu.edu
-
-# Datasets in an error state include a link to report the error. Those reports
-# will be sent to this address. Error reports are disabled if no address is set.
-#error_email_to = None
-
-# -- Display sites
-
-# Galaxy can display data at various external browsers. These options specify
-# which browsers should be available. URLs and builds available at these
-# browsers are defined in the specifield files.
-
-# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
-#ucsc_display_sites = main,test,archaea,ucla
-
-# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
-#gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd
-
-# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
-#genetrack_display_sites = main,test
-
-# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.
-
-use_nglims = False
-nglims_config_file = tool-data/nglims.yaml
-
-# -- UI Localization
-
-# Append "/{brand}" to the "Galaxy" text in the masthead.
-#brand = None
-
-# The URL linked by the "Galaxy/brand" text.
-#logo_url = /
-
-# The URL linked by the "Galaxy Wiki" link in the "Help" menu.
-#wiki_url = http://wiki.g2.bx.psu.edu/
-
-# The URL linked by the "Support" link in the "Help" menu.
-#support_url = http://wiki.g2.bx.psu.edu/Support
-
-# The URL linked by the "How to Cite..." link in the "Help" menu.
-#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy
-
-# Serve static content, which must be enabled if you're not serving it via a
-# proxy server. These options should be self explanatory and so are not
-# documented individually. You can use these paths (or ones in the proxy
-# server) to point to your own styles.
-static_enabled = True
-static_cache_time = 360
-static_dir = %(here)s/static/
-static_images_dir = %(here)s/static/images
-static_favicon_dir = %(here)s/static/favicon.ico
-static_scripts_dir = %(here)s/static/scripts/
-static_style_dir = %(here)s/static/june_2007_style/blue
-static_robots_txt = %(here)s/static/robots.txt
-
-# Pack javascript at launch (/static/scripts/*.js)
-# This only happens if the modified timestamp of the source .js is newer
-# than the version (if it exists) in /static/scripts/packed/
-# Note that this requires java > 1.4 for executing yuicompressor.jar
-#pack_scripts = False
-
-# Enable Cloud Launch
-
-#enable_cloud_launch = False
-
-# -- Advanced proxy features
-
-# For help on configuring the Advanced proxy features, see:
-# http://usegalaxy.org/production
-
-# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set
-# this to True to inform Galaxy that mod_xsendfile is enabled upstream.
-#apache_xsendfile = False
-
-# The same download handling can be done by nginx using X-Accel-Redirect. This
-# should be set to the path defined in the nginx config as an internal redirect
-# with access to Galaxy's data files (see documentation linked above).
-#nginx_x_accel_redirect_base = False
-
-# nginx can make use of mod_zip to create zip files containing multiple library
-# files. If using X-Accel-Redirect, this can be the same value as that option.
-#nginx_x_archive_files_base = False
-
-# If using compression in the upstream proxy server, use this option to disable
-# gzipping of library .tar.gz and .zip archives, since the proxy server will do
-# it faster on the fly.
-#upstream_gzip = False
-
-# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
-# Configuration for this is complex and explained in detail in the
-# documentation linked above. The upload store is a temporary directory in
-# which files uploaded by the upload module will be placed.
-#nginx_upload_store = False
-
-# This value overrides the action set on the file upload form, e.g. the web
-# path where the nginx_upload_module has been configured to intercept upload
-# requests.
-#nginx_upload_path = False
-
-# -- Logging and Debugging
-
-# Verbosity of console log messages. Acceptable values can be found here:
-# http://docs.python.org/library/logging.html#logging-levels
-#log_level = DEBUG
-
-# Print database operations to the server log (warning, quite verbose!).
-#database_engine_option_echo = False
-
-# Print database pool operations to the server log (warning, quite verbose!).
-#database_engine_option_echo_pool = False
-
-# Turn on logging of application events and some user events to the database.
-#log_events = True
-
-# Turn on logging of user actions to the database. Actions currently logged are
-# grid views, tool searches, and use of "recently" used tools menu. The
-# log_events and log_actions functionality will eventually be merged.
-#log_actions = True
-
-# Sanitize All HTML Tool Output
-# By default, all tool output served as 'text/html' will be sanitized
-# thoroughly. This can be disabled if you have special tools that require
-# unaltered output.
-#sanitize_all_html = True
-
-# Debug enables access to various config options useful for development and
-# debugging: use_lint, use_profile, use_printdebug and use_interactive. It
-# also causes the files used by PBS/SGE (submission script, output, and error)
-# to remain on disk after the job is complete. Debug mode is disabled if
-# commented, but is uncommented by default in the sample config.
-debug = True
-
-# Check for WSGI compliance.
-#use_lint = False
-
-# Run the Python profiler on each request.
-#use_profile = False
-
-# Intercept print statements and show them on the returned page.
-#use_printdebug = True
-
-# Enable live debugging in your browser. This should NEVER be enabled on a
-# public site. Enabled in the sample config for development.
-use_interactive = True
-
-# Write thread status periodically to 'heartbeat.log', (careful, uses disk
-# space rapidly!). Useful to determine why your processes may be consuming a
-# lot of CPU.
-#use_heartbeat = False
-
-# Enable the memory debugging interface (careful, negatively impacts server
-# performance).
-#use_memdump = False
-
-# -- Data Libraries
-
-# These library upload options are described in much more detail in the wiki:
-# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
-
-# Add an option to the library upload form which allows administrators to
-# upload a directory of files.
-#library_import_dir = None
-
-# Add an option to the library upload form which allows authorized
-# non-administrators to upload a directory of files. The configured directory
-# must contain sub-directories named the same as the non-admin user's Galaxy
-# login ( email ). The non-admin user is restricted to uploading files or
-# sub-directories of files contained in their directory.
-#user_library_import_dir = None
-
-# Add an option to the admin library upload tool allowing admins to paste
-# filesystem paths to files and directories in a box, and these paths will be
-# added to a library. Set to True to enable. Please note the security
-# implication that this will give Galaxy Admins access to anything your Galaxy
-# user has access to.
-#allow_library_path_paste = False
-
-# Users may choose to download multiple files from a library in an archive. By
-# default, Galaxy allows users to select from a few different archive formats
-# if testing shows that Galaxy is able to create files using these formats.
-# Specific formats can be disabled with this option, separate more than one
-# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'.
-#disable_library_comptypes =
-
-# Some sequencer integration features in beta allow you to automatically
-# transfer datasets. This is done using a lightweight transfer manager which
-# runs outside of Galaxy (but is spawned by it automatically). Galaxy will
-# communicate with this manager over the port specified here.
-#transfer_manager_port = 8163
-
-# Search data libraries with whoosh
-#enable_whoosh_library_search = True
-# Whoosh indexes are stored in this directory.
-#whoosh_index_dir = database/whoosh_indexes
-
-# Search data libraries with lucene
-#enable_lucene_library_search = False
-# maxiumum file size to index for searching, in MB
-#fulltext_max_size = 500
-#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
-# base URL of server providing search functionality using lucene
-#fulltext_url = http://localhost:8081
-
-# -- Users and Security
-
-# Galaxy encodes various internal values when these values will be output in
-# some format (for example, in a URL or cookie). You should set a key to be
-# used by the algorithm that encodes and decodes these values. It can be any
-# string. If left unchanged, anyone could construct a cookie that would grant
-# them access to others' sessions.
-#id_secret = USING THE DEFAULT IS NOT SECURE!
-
-# User authentication can be delegated to an upstream proxy server (usually
-# Apache). The upstream proxy should set a REMOTE_USER header in the request.
-# Enabling remote user disables regular logins. For more information, see:
-# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
-#use_remote_user = False
-
-# If use_remote_user is enabled and your external authentication
-# method just returns bare usernames, set a default mail domain to be appended
-# to usernames, to become your Galaxy usernames (email addresses).
-#remote_user_maildomain = None
-
-# If use_remote_user is enabled, you can set this to a URL that will log your
-# users out.
-#remote_user_logout_href = None
-
-# Administrative users - set this to a comma-separated list of valid Galaxy
-# users (email addresses). These users will have access to the Admin section
-# of the server, and will have access to create users, groups, roles,
-# libraries, and more. For more information, see:
-# http://wiki.g2.bx.psu.edu/Admin/Interface
-#admin_users = None
-
-# Force everyone to log in (disable anonymous access).
-#require_login = False
-
-# Allow unregistered users to create new accounts (otherwise, they will have to
-# be created by an admin).
-#allow_user_creation = True
-
-# Allow administrators to delete accounts.
-#allow_user_deletion = False
-
-# Allow administrators to log in as other users (useful for debugging)
-#allow_user_impersonation = False
-
-# Allow users to remove their datasets from disk immediately (otherwise,
-# datasets will be removed after a time period specified by an administrator in
-# the cleanup scripts run via cron)
-#allow_user_dataset_purge = False
-
-# By default, users' data will be public, but setting this to True will cause
-# it to be private. Does not affect existing users and data, only ones created
-# after this option is set. Users may still change their default back to
-# public.
-#new_user_dataset_access_role_default_private = False
-
-# -- Beta features
-
-# Object store mode (valid options are: disk, s3, distributed, hierarchical)
-#object_store = disk
-#aws_access_key = <AWS access key>
-#aws_secret_key = <AWS secret key>
-#s3_bucket = <name of an existing S3 bucket>
-#use_reduced_redundancy = True
-
-# Size (in GB) that the cache used by object store should be limited to.
-# If the value is not specified, the cache size will be limited only by the file
-# system size.
-#object_store_cache_size = 100
-
-# Configuration file for the distributed object store, if object_store =
-# distributed. See the sample at distributed_object_store_conf.xml.sample
-#distributed_object_store_config_file = None
-
-# Enable Galaxy to communicate directly with a sequencer
-#enable_sequencer_communication = False
-
-# Enable Galaxy's built-in visualization module, Trackster.
-#enable_tracks = True
-
-# Enable Galaxy Pages. Pages are custom webpages that include embedded Galaxy items,
-# such as datasets, histories, workflows, and visualizations; pages are useful for
-# documenting and sharing multiple analyses or workflows. Pages are created using a
-# WYSIWYG editor that is very similar to a word processor.
-#enable_pages = True
-
-# Enable authentication via OpenID. Allows users to log in to their Galaxy
-# account by authenticating with an OpenID provider.
-#enable_openid = False
-
-# Enable the (experimental! beta!) Web API. Documentation forthcoming.
-#enable_api = False
-
-# Optional list of email addresses of API users who can make calls on behalf of
-# other users
-#api_allow_run_as = None
-
-# Enable tool tags (associating tools with tags). This has its own option
-# since its implementation has a few performance implications on startup for
-# large servers.
-#enable_tool_tags = False
-
-# Enable a feature when running workflows. When enabled, default datasets
-# are selected for "Set at Runtime" inputs from the history such that the
-# same input will not be selected twice, unless there are more inputs than
-# compatible datasets in the history.
-# When False, the most recently added compatible item in the history will
-# be used for each "Set at Runtime" input, independent of others in the Workflow
-#enable_unique_workflow_defaults = False
-
-# Enable Galaxy's "Upload via FTP" interface. You'll need to install and
-# configure an FTP server (we've used ProFTPd since it can use Galaxy's
-# database for authentication) and set the following two options.
-
-# This should point to a directory containing subdirectories matching users'
-# email addresses, where Galaxy will look for files.
-#ftp_upload_dir = None
-
-# This should be the hostname of your FTP server, which will be provided to
-# users in the help text.
-#ftp_upload_site = None
-
-# Enable enforcement of quotas. Quotas can be set from the Admin interface.
-#enable_quotas = False
-
-# Enable a feature when running workflows. When enabled, default datasets
-# are selected for "Set at Runtime" inputs from the history such that the
-# same input will not be selected twice, unless there are more inputs than
-# compatible datasets in the history.
-# When False, the most recently added compatible item in the history will
-# be used for each "Set at Runtime" input, independent of others in the Workflow
-#enable_unique_workflow_defaults = False
-
-# -- Job Execution
-
-# If running multiple Galaxy processes, one can be designated as the job
-# runner. For more information, see:
-# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
-#enable_job_running = True
-
-# Should jobs be tracked through the database, rather than in memory.
-# Necessary if you're running the load balanced setup.
-#track_jobs_in_database = False
-
-# This enables splitting of jobs into tasks, if specified by the particular tool config.
-# This is a new feature and not recommended for production servers yet.
-#use_tasked_jobs = False
-#local_task_queue_workers = 2
-
-# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
-# it can "recover" them when it starts). This is not safe to use if you are
-# running more than one Galaxy server using the same database.
-#enable_job_recovery = True
-
-# Setting metadata on job outputs to in a separate process (or if using a
-# cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the
-# hefty expense that setting metadata incurs, your Galaxy process may become
-# unresponsive when this operation occurs internally.
-#set_metadata_externally = False
-
-# Although it is fairly reliable, setting metadata can occasionally fail. In
-# these instances, you can choose to retry setting it internally or leave it in
-# a failed state (since retrying internally may cause the Galaxy process to be
-# unresponsive). If this option is set to False, the user will be given the
-# option to retry externally, or set metadata manually (when possible).
-#retry_metadata_internally = True
-
-# If (for example) you run on a cluster and your datasets (by default,
-# database/files/) are mounted read-only, this option will override tool output
-# paths to write outputs to the working directory instead, and the job manager
-# will move the outputs to their proper place in the dataset directory on the
-# Galaxy server after the job completes.
-#outputs_to_working_directory = False
-
-# If your network filesystem's caching prevents the Galaxy server from seeing
-# the job's stdout and stderr files when it completes, you can retry reading
-# these files. The job runner will retry the number of times specified below,
-# waiting 1 second between tries. For NFS, you may want to try the -noac mount
-# option (Linux) or -actimeo=0 (Solaris).
-#retry_job_output_collection = 0
-
-# Clean up various bits of jobs left on the filesystem after completion. These
-# bits include the job working directory, external metadata temporary files,
-# and DRM stdout and stderr files (if using a DRM). Possible values are:
-# always, onsuccess, never
-#cleanup_job = always
-
-# Number of concurrent jobs to run (local job runner)
-#local_job_queue_workers = 5
-
-# Jobs can be killed after a certain amount of execution time. Format is in
-# hh:mm:ss. Currently only implemented for PBS.
-#job_walltime = None
-
-# Jobs can be killed if any of their outputs grow over a certain size (in
-# bytes). 0 for no limit.
-#output_size_limit = 0
-
-# Clustering Galaxy is not a straightforward process and requires some
-# pre-configuration. See the the wiki before attempting to set any of these
-# options:
-# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
-
-# Comma-separated list of job runners to start. local is always started. If
-# left commented, no jobs will be run on the cluster, even if a cluster URL is
-# explicitly defined in the [galaxy:tool_runners] section below. The runners
-# currently available are 'pbs' and 'drmaa'.
-#start_job_runners = None
-
-# For sites where all users in Galaxy match users on the system on which Galaxy
-# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the
-# actual user instead of as the user running the Galaxy server process. For
-# details on these options, see the documentation at:
-#
-# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster
-#
-#drmaa_external_runjob_script = scripts/drmaa_external_runner.py
-#drmaa_external_killjob_script = scripts/drmaa_external_killer.py
-#external_chown_script = scripts/external_chown_script.py
-
-# File to source to set up the environment when running jobs. By default, the
-# environment in which the Galaxy server starts is used when running jobs
-# locally, and the environment set up per the DRM's submission method and
-# policy is used when running jobs on a cluster (try testing with `qsub` on the
-# command line). environment_setup_file can be set to the path of a file on
-# the cluster that should be sourced by the user to set up the environment
-# prior to running tools. This can be especially useful for running jobs as
-# the actual user, to remove the need to configure each user's environment
-# individually. This only affects cluster jobs, not local jobs.
-#environment_setup_file = None
-
-# The URL for the default runner to use when a tool doesn't explicitly define a
-# runner below.
-#default_cluster_job_runner = local:///
-
-# The cluster runners have their own thread pools used to prepare and finish
-# jobs (so that these sometimes lengthy operations do not block normal queue
-# operation). The value here is the number of worker threads available to each
-# started runner.
-#cluster_job_queue_workers = 3
-
-# These options are only used when using file staging with PBS.
-#pbs_application_server =
-#pbs_stage_path =
-#pbs_dataset_server =
-
-# ---- Tool Job Runners -----------------------------------------------------
-
-# Individual per-tool job runner overrides. Parameters can be included to define
-# multiple runners per tool. E.g. to run Cufflinks jobs initiated from Trackster
-# differently than standard Cufflinks jobs:
-# cufflinks = local:///
-# cufflinks[source at trackster] = local:///
-# If not listed here, a tool will run with the runner defined with
-# default_cluster_job_runner.
-
-[galaxy:tool_runners]
-
-biomart = local:///
-encode_db1 = local:///
-hbvar = local:///
-microbial_import1 = local:///
-ucsc_table_direct1 = local:///
-ucsc_table_direct_archaea1 = local:///
-ucsc_table_direct_test1 = local:///
-upload1 = local:///
-
-# ---- Galaxy Message Queue -------------------------------------------------
-
-# Galaxy uses AMQ protocol to receive messages from external sources like
-# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
-# For Galaxy to receive messages from a message queue the RabbitMQ server has
-# to be set up with a user account and other parameters listed below. The 'host'
-# and 'port' fields should point to where the RabbitMQ server is running.
-
-[galaxy_amqp]
-
-#host = 127.0.0.1
-#port = 5672
-#userid = galaxy
-#password = galaxy
-#virtual_host = galaxy_messaging_engine
-#queue = galaxy_queue
-#exchange = galaxy_exchange
-#routing_key = bar_code_scanner
-#rabbitmqctl_path = /path/to/rabbitmqctl
-
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