Re: [galaxy-dev] How to get cleanup script to run in cron job ?
Hi, Try this : 55 21 * * * cd /media/Store/galaxy/galaxy-dist/ python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i /media/Store/galaxy/galaxy-dist/temp 21 I thought you need to be in the galaxy-dist folder when launching the commands. Best, Geert On 11/19/2014 11:14 PM, James Mullan wrote: Hello, I am trying to figure out how to run the cleanup scripts in a cron job. The below works on command line: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i pysqlite=2 egg successfully loaded for sqlite dialect ## # 2014-11-19 22:07:32 - Handling stuff older than 30 days # Displaying info only ( --info_only ) Deleted 0 histories Elapsed time: 0.0684289932251 ## but if I try to do this in a cron job as follows: 55 21 * * * python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i /media/Store/galaxy/galaxy-dist/temp 21 python: can't open file 'scripts/cleanup_datasets/cleanup_datasets.py': [Errno 2] No such file or directory or if I try to do this : 00 22 * * * python /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i /media/Store/galaxy/galaxy-dist/temp 21 Traceback (most recent call last): File /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py, line 13, in module from galaxy import eggs ImportError: No module named galaxy Note that I am directing the output to a file only to try to find out why it's not working. Is this a problem with environment? Any suggestions what to try would be much appreciated. Regards James J P Mullan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Local Galaxy Apache Config
Hello Galaxy Admins,
I am attempting to setup a local production-grade Galaxy server for
our department. Before I go ahead and turn on Galaxy for the first
time, would you be so kind as to please review my Apache2 config files
for errors? I want to be sure that things are in the correct place to
save me from headaches down the road.
The overall goals of the configuration are:
- always use HTTPS and secure FTP
- make maximum use of the machine (multiple Apache processes,
PostgreSQL, ProFTPD, etc.)
If it helps, Galaxy will be running on a:
- Dell Precision T7500
- 2 x Intel Xeon X5690 @ 3.46 GHz
- 96 GB RAM
- Ubuntu 14.04 64-bit
Thank you for your help!
FYI: My config files are based on the instructions at
https://wiki.galaxyproject.org/Admin/GetGalaxy and
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
##
#
# /etc/apache2/apache2.conf
#
##
# Global configuration
#
# ServerRoot: The top of the directory tree under which the server's
# configuration, error, and log files are kept.
#
# NOTE! If you intend to place this on an NFS (or otherwise network)
# mounted filesystem then please read the Mutex documentation (available
# at URL:http://httpd.apache.org/docs/2.4/mod/core.html#mutex);
# you will save yourself a lot of trouble.
#
# Do NOT add a slash at the end of the directory path.
#
#ServerRoot /etc/apache2
#
# The accept serialization lock file MUST BE STORED ON A LOCAL DISK.
#
Mutex file:${APACHE_LOCK_DIR} default
#
# PidFile: The file in which the server should record its process
# identification number when it starts.
# This needs to be set in /etc/apache2/envvars
#
PidFile ${APACHE_PID_FILE}
#
# Timeout: The number of seconds before receives and sends time out.
#
Timeout 300
#
# KeepAlive: Whether or not to allow persistent connections (more than
# one request per connection). Set to Off to deactivate.
#
KeepAlive On
#
# MaxKeepAliveRequests: The maximum number of requests to allow
# during a persistent connection. Set to 0 to allow an unlimited amount.
# We recommend you leave this number high, for maximum performance.
#
MaxKeepAliveRequests 100
#
# KeepAliveTimeout: Number of seconds to wait for the next request from the
# same client on the same connection.
#
KeepAliveTimeout 5
# These need to be set in /etc/apache2/envvars
User ${APACHE_RUN_USER}
Group ${APACHE_RUN_GROUP}
#
# HostnameLookups: Log the names of clients or just their IP addresses
# e.g., www.apache.org (on) or 204.62.129.132 (off).
# The default is off because it'd be overall better for the net if people
# had to knowingly turn this feature on, since enabling it means that
# each client request will result in AT LEAST one lookup request to the
# nameserver.
#
HostnameLookups Off
# ErrorLog: The location of the error log file.
# If you do not specify an ErrorLog directive within a VirtualHost
# container, error messages relating to that virtual host will be
# logged here. If you *do* define an error logfile for a VirtualHost
# container, that host's errors will be logged there and not here.
#
ErrorLog ${APACHE_LOG_DIR}/error.log
#
# LogLevel: Control the severity of messages logged to the error_log.
# Available values: trace8, ..., trace1, debug, info, notice, warn,
# error, crit, alert, emerg.
# It is also possible to configure the log level for particular modules, e.g.
# LogLevel info ssl:warn
#
LogLevel warn
# Include module configuration:
IncludeOptional mods-enabled/*.load
IncludeOptional mods-enabled/*.conf
# Include list of ports to listen on
Include ports.conf
# Sets the default security model of the Apache2 HTTPD server. It does
# not allow access to the root filesystem outside of /usr/share and /var/www.
# The former is used by web applications packaged in Debian,
# the latter may be used for local directories served by the web server. If
# your system is serving content from a sub-directory in /srv you must allow
# access here, or in any related virtual host.
Directory /
Options FollowSymLinks
AllowOverride None
Require all denied
/Directory
Directory /usr/share
AllowOverride None
Require all granted
/Directory
Directory /var/www/
Options Indexes FollowSymLinks
AllowOverride None
Require all granted
/Directory
#Directory /srv/
#Options Indexes FollowSymLinks
#AllowOverride None
#Require all granted
#/Directory
# AccessFileName: The name of the file to look for in each directory
# for additional configuration directives. See also the AllowOverride
# directive.
#
AccessFileName .htaccess
#
# The following lines prevent .htaccess and .htpasswd files from being
# viewed by Web clients.
#
FilesMatch ^\.ht
Require all denied
/FilesMatch
#
# The following directives define some format nicknames for use with
# a CustomLog directive.
#
# These deviate from the Common Log Format definitions in that they use %O
# (the actual bytes sent including headers) instead of %b
Re: [galaxy-dev] Problem with LWR (input size limitation)
Hi John , First all, thank you very much for your quick reply. I will test your suggestion about pycurl, and tell you if it has worked. For the second question, i was wondering if it is possible with LWR to define a path (where are located the inputs) as an input (string input in the wrapper xml). Thank you again for your help, Misharl Monsoor. Le 19/11/2014 15:30, John Chilton a écrit : If you install pycurl (globally or in a Galaxy's virtualenv) and set LWR_CURL_TRANSPORT=1 in Galaxy's environment than the LWR will stream large files with CURL instead of the mmap hack. I don't understand your second question - the LWR should stream whatever data inputs are selected by the user. If you want the tool to be able to take many inputs you can use multiple=true on your data parameter or use a repeat block. (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax). Hope this helps, -John On Mon, Nov 17, 2014 at 3:04 AM, Misharl Monsoor mmons...@sb-roscoff.fr wrote: Hi everybody, In our lab, we are trying to connect our Galaxy instance to a Windows 7 64 bits server, in order to executes programs that need to be run within Windows. However we have a problem concerning the size of the input that is uploaded to the Windows server, it doesn't accept inputs with a size 1.3 Gb ? We have the following problem with mmap function: data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) error: [Errno 12] Cannot allocate memory I have another question concerning the inputs, is there a way to use several inputs that be uploaded to a Windows Server? Thank you very much in advance, Bests regards, Cheers, Misharl Monsoor ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
