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Events/GCC2014/TrainingDay/AdminWalkthrough

Tutorial: Galaxy Installation and Administration

Nate Coraor and John Chilton


https://dev.twitter.com/sites/default/files/images_documentation/bird_blue_16.png #usegalaxy

This this follow-along page assumes you have already installed and started a Training Day VM - please do this before arriving.

This tool assumes you are using Firefox bundled with the VM. Galaxy is compatible with all modern versions of Firefox, Chrome, Safari, and Internet Explorer. However, for the purposes of this tutorial it will help us when assisting people encountering problems if they are only using Firefox.

Setting up a Local Galaxy Tutorial (Part I)

Clone (download) Galaxy

The Galaxy distribution is found at https://bitbucket.org/galaxy/galaxy-dist/, but for the purposes of this tutorial, we'll use a local copy already on the VM to save time.

   1 galaxy@gcc2014:~$ hg clone /home/galaxy/galaxy-central galaxy-dist
   2 requesting all changes
   3 adding changesets
   4 adding manifests
   5 adding file changes
   6 added 8 changesets with 3443 changes to 3443 files
   7 updating to branch default
   8 3443 files updated, 0 files merged, 0 files removed, 0 files unresolved
   9 galaxy@gcc2014:~$ cd galaxy-dist
  10 galaxy@gcc2014:~/galaxy-dist$

References

Update to the stable branch

   1 galaxy@gcc2014:~$ cd galaxy-dist
   2 galaxy@gcc2014:~/galaxy-dist$ hg update stable
   3 264 files updated, 0 files merged, 144 files removed, 0 files unresolved
   4 galaxy@gcc2014:~/galaxy-dist$

Start Galaxy

   1 galaxy@gcc2014:~/galaxy-dist$ cp -r ../galaxy-central/eggs eggs  # cache dependencies to speed up deploy (optional)
   2 galaxy@gcc2014:~/galaxy-dist$ sh run.sh
   3 Initializing datatypes_conf.xml from datatypes_conf.xml.sample
   4   ...
   5 Some eggs are out of date, attempting to fetch...
   6 Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.3-py2.7.egg
   7   ...
   8 Fetch successful.
   9 python path is: /home/ubuntu/galaxy-dist/eggs/mercurial-2...
  10   ...
  11 Starting server in PID 3091.
  12 serving on http://127.0.0.1:8080
  13 

Serve over public interface

Stop Galaxy by hitting CTRL-c:

   1 serving on http://127.0.0.1:8080
   2 ^Cgalaxy.jobs.handler INFO 2014-04-23 13:27:59,203 sending stop signal to worker thread
   3 galaxy.jobs.handler INFO 2014-04-23 13:27:59,204 job handler queue stopped
   4 galaxy.jobs.runners INFO 2014-04-23 13:27:59,204 LWRRunner: Sending stop signal to monitor thread
   5 galaxy.jobs.runners INFO 2014-04-23 13:27:59,204 LWRRunner: Sending stop signal to 3 worker threads
   6 galaxy.jobs.runners INFO 2014-04-23 13:27:59,204 LocalRunner: Sending stop signal to 5 worker threads
   7 galaxy.jobs.handler INFO 2014-04-23 13:27:59,205 sending stop signal to worker thread
   8 galaxy.jobs.handler INFO 2014-04-23 13:27:59,205 job handler stop queue stopped
   9 galaxy@gcc2014:~/galaxy-dist$

There may be some additional interruption exceptions reported - these are not important.

Edit the primary Galaxy configuration file, universe_wsgi.ini. If you are not familiar with vi, consider using nano instead.

   1 galaxy@gcc2014:~/galaxy-dist$ vi universe_wsgi.ini

In the [server:main] section, uncomment #host = 127.0.0.1 and set:

   1 host = 0.0.0.0

While we are in the config, we should set two options necessary for the next section. The file is large and it's easiest to search for these (/<pattern> in vi, CTRL-w <pattern> in nano):

   1 [app:main]
   2 admin_users = nate@bx.psu.edu
   3 tool_dependency_dir = /home/galaxy/tool_deps

Then save and quit (CTRL-x y ENTER in nano). Start Galaxy again:

   1 galaxy@gcc2014:~/galaxy-dist$ sh run.sh 
   2   ...
   3 Starting server in PID 3298.
   4 serving on 0.0.0.0:8080 view at http://127.0.0.1:8080
   5 

The message view at http://127.0.0.1:8080 is generated by the embedded webserver and cannot be changed so it is not entirely accurate, but serving on 0.0.0.0:8080 reveals that the server is now listening on public interfaces.

Installing tools from the Tool Shed

Topics for this section

  • What is a Galaxy tool?
    • Basic: An XML description of the tool's interface, allowing Galaxy to render a UI (tool form), as well as the command line to execute.
    • Complex: XML + wrapper scripts and interfaces to external dependencies
  • Exploring preinstalled tools and filesystem layout
    • galaxy-dist/tool_conf.xml

    • galaxy-dist/tools/

    • Example simple tool: galaxy-dist/tools/filters/sorter.xml (tool xml), galaxy-dist/tools/filters/sorter.py (tool code)

    • Example tool with unmet dependencies: galaxy-dist/tools/sr_mapping/mosaik.xml

  • The Tool Shed
    • Installing tools from the Tool Shed
    • Exploring the filesystem layout of tools installed from the Tool Shed

Install a tool from the Tool Shed

You will need to enable 3rd-party cookies in your browser for Tool Shed installations to work:

  • Firefox: Edit -> Preferences -> Privacy -> History -> Firefox will: Remember history or Firefox will: Use custom settings for history -> Accept third-party cookies: Always

Reload the Galaxy interface if your 3rd party cookies were not previously enabled.


  • Register an account that matches the address you set in admin_users

  • Follow the tutorial on installing tools from the Tool Shed. In brief:

    • Click Admin from the masthead

    • Click Search and browse tool sheds from the left panel

    • Click the popup icon for Galaxy main tool shed and select Search for valid tools

    • Search for Tool names that contain the name bwa

    • Click the popup icon for bwa_wrappers and select Install to Galaxy

    • Select the NGS: Mapping section and click Install to Galaxy

  • Tools (XML, wrapper scripts) are installed in /home/galaxy/shed_tools

  • Tool dependencies (binaries) are installed in /home/galaxy/tool_deps

References

Managing local data

Topics for this section

  • What is local data?
  • Manual data inclusion
    • Building indexes on the command line
    • .loc files

    • tool_data_table_conf.xml

    • Example of the above with bwa and S. cerevisiae (sacCer2) transcript

  • Galaxy Data Managers

Adding local data with a Galaxy Data Manager

Install data managers for fetching the reference genome and building BWA indexes:

  • Click Admin from the masthead

  • Click Search and browse tool sheds from the left panel

  • Click the popup icon for Galaxy main tool shed and select Search for valid tools

  • Search for Tool ids that contain the name manager

  • Check data_manager_fetch_genome_all_fasta and data_manager_bwa_index_builder, then click Install to Galaxy (at the bottom of the page)

  • Click Install

Fetch reference genome (fasta):

  • Click Manage local data (beta) from the left panel

  • Click Reference Genome - fetching

  • In the DBKEY to assign to data: field, type sacCer2

  • In the UCSC's DBKEY for source FASTA: field, type sacCer2

  • Click Execute

Build BWA indexes:

  • Click Manage local data (beta) from the left panel

  • Click BWA index - builder

  • Click Execute

Upon completion:

  • galaxy-dist/tool-data/sacCer2/seq/sacCer2.fa has been created from chromosome fastas fetched from UCSC

  • galaxy-dist/tool-data/sacCer2/bwa_index/sacCer2.fa.* indexes have been generated with bwa index

  • galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/all_fasta.loc contains a reference to the newly created sacCer2.fa

  • galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_index_builder/367878cb3698/bwa_index.loc contains a reference to the newly built bwa indexes

  • galaxy-dist/shed_tool_data_table_conf.xml includes entries for the all_fasta and bwa_indexes data tables

References

Setting up a Local Galaxy Tutorial (Part II)

Documentation for the features used in this section can be found at usegalaxy.org/production (forwards to Admin/Config/Performance/ProductionServer)

Install and configure PostgreSQL

galaxy@gcc2014:~/galaxy-dist$ sudo apt-get install postgresql
[sudo] password for galaxy: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
postgresql is already the newest version.
...
galaxy@gcc2014:~/galaxy-dist$ sudo -u postgres createuser gxprod
galaxy@gcc2014:~/galaxy-dist$ sudo -u postgres createdb -O gxprod gxprod

Create a new user for Galaxy

   1 galaxy@gcc2014:~/galaxy-dist$ sudo useradd -m -s /bin/bash gxprod
   2 galaxy@gcc2014:~/galaxy-dist$ 

Create a Python virtual environment

   1 galaxy@gcc2014:~/galaxy-dist$ sudo apt-get install python-virtualenv
   2 Reading package lists... Done
   3 Building dependency tree
   4 Reading state information... Done
   5 The following extra packages will be installed:
   6   ...
   7 Do you want to continue? [Y/n]
   8   ...
   9 Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty/main libasan0 amd64 4.8.2-19ubuntu1 [63.0 kB]
  10   ...
  11 Processing triggers for libc-bin (2.19-0ubuntu6) ...
  12 galaxy@gcc2014:~/galaxy-dist$ sudo -iu gxprod
  13 gxprod@gcc2014:~$ virtualenv venv
  14 New python executable in venv/bin/python
  15 Installing setuptools, pip...done.
  16 gxprod@gcc2014:~$ source ./venv/bin/activate
  17 (venv)gxprod@gcc2014:~$ 

Clone (download) Galaxy

   1 gxprod@gcc2014:~$ hg clone ~galaxy/galaxy-central galaxy-dist
   2 not trusting file /home/galaxy/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy
   3 requesting all changes
   4 adding changesets
   5 adding manifests
   6 adding file changes
   7 added 13944 changesets with 47333 changes to 8458 files
   8 updating to branch default
   9 3658 files updated, 0 files merged, 0 files removed, 0 files unresolved
  10 gxprod@gcc2014:~/galaxy-dist$ hg update stable
  11 264 files updated, 0 files merged, 144 files removed, 0 files unresolved
  12 gxprod@gcc2014:~/galaxy-dist$ cp -r ~galaxy/galaxy-central/eggs .
  13 0 files updated, 0 files merged, 0 files removed, 0 files unresolved
  14 gxprod@gcc2014:~/galaxy-dist$ 

Configure Galaxy

   1 gxprod@gcc2014:~/galaxy-dist$ cp universe_wsgi.ini.sample universe_wsgi.ini
   2 gxprod@gcc2014:~/galaxy-dist$ vi universe_wsgi.ini

Add the following section for uWSGI's configuration and the job handler processes

   1 [uwsgi]
   2 socket = 127.0.0.1:4001
   3 stats = 127.0.0.1:9191
   4 processes = 2
   5 threads = 4
   6 master = True
   7 logto = /home/gxprod/uwsgi.log
   8 pythonpath = lib
   9 
  10 [server:handler0]
  11 use = egg:Paste#http
  12 port = 9010
  13 use_threadpool = True
  14 threadpool_workers = 10
  15 
  16 [server:handler1]
  17 use = egg:Paste#http
  18 port = 9011
  19 use_threadpool = True
  20 threadpool_workers = 10

Set the following settings in the [app:main] section:

   1 database_connection = postgresql:///gxprod?host=/var/run/postgresql
   2 database_engine_option_server_side_cursors = True
   3 database_engine_option_strategy = threadlocal
   4 tool_dependency_dir = /home/gxprod/tool_deps
   5 static_enabled = False
   6 nginx_x_accel_redirect_base = /_x_accel_redirect
   7 nginx_upload_store = /home/gxprod/uploads
   8 nginx_upload_path = /_upload
   9 log_events = False
  10 log_actions = False
  11 debug = False
  12 use_interactive = False
  13 id_secret = <random text>
  14 admin_users = nate@bx.psu.edu

Explanations of these options:

  • database_connection = postgresql:///gxprod?host=/var/run/postgresql - Use a PostgreSQL database via a local UNIX domain socket (the socket is in /var/run/postgresql). documentation

  • database_engine_option_server_side_cursors = True - Keep large SQL query results on the PostgreSQL server, rather the transferring the entire result set to the Galaxy processes.

  • database_engine_option_strategy = threadlocal - Only use one database connection per thread

  • tool_dependency_dir = /home/gxprod/tool_deps - The directory that will house tool dependencies

  • static_enabled = False - Static content will be served by the proxy server

  • nginx_x_accel_redirect_base = /_x_accel_redirect - Delegate dataset downloads to nginx

  • nginx_upload_store = /home/gxprod/uploads - Delegate uploads to nginx, set temporary directory

  • nginx_upload_path = /_upload - Special path configured in nginx where uploads will be POSTed

  • log_events = False - Don't log events in the database (faster)

  • log_actions = False - Don't log actions in the database (faster)

  • debug = False - Disables debugging middleware that loads server responses in to memory (can crash the server when handling large files)

  • use_interactive = False - Disables live client browser debugging (insecure).

  • id_secret = <random text> - Ensures that the encoded IDs used by Galaxy (especially session IDs) are unique. One simple way to generate a value for this is with a shell command like $ date | md5sum

  • admin_users = nate@bx.psu.edu - Make nate@example.org an administrator. Galaxy's Admin UI is only accessible if you define administrators here!

Honorable mentions for features we won't use today but that are common in big setups:

  • ftp_upload_dir and ftp_upload_site - Allow users to upload data to the server using FTP

  • use_remote_user and remote_user_maildomain - Use your institution's existing authentication system to log in to Galaxy. Apache documentation or nginx documentation

  • allow_user_impersonation - Users configured as administrators (with admin_users) can "become" other users to view Galaxy exactly as the impersonated user does. Useful for providing support.

  • library_import_dir - Administrators can directly import datasets from this directory on the server to Data Libraries. This includes an option that allows an effective "symlink" to the data, rather than copying it in to Galaxy's file_path directory. documentation

  • user_library_import_dir - Non-administrators can directly import datasets from this directory on this server to Data Libraries from which they have been given write permission. documentation

  • allow_library_path_paste - Administrators can import datasets from anywhere on the server's filesystem(s) by entering their paths in to a text box

  • object_store_config_file - Configure Galaxy's "object storage" layer to store data in multiple filesystems, Amazon S3, iRODS, etc.

  • error_email_to (with smtp_server) - Allow users to send bug reports directly to you

  • user_activation_on and related options - Require new users to verify their email address

  • allow_user_dataset_purge = True - Allow users to forcibly remove their datasets from disk (note that the data is only actually removed if all versions of a shared dataset are purged by all users who are sharing the dataset). By default, Galaxy does not remove data, as this is done at a later time by the dataset cleanup scripts.

  • enable_quotas = True - Enable Galaxy's quota system. Quotas are configured by administrators in the Galaxy Admin UI

Create a job system configuration:

   1 gxprod@gcc2014:~/galaxy-dist$ vi job_conf.xml

In the editor, paste:

   1 <?xml version="1.0"?>
   2 <job_conf>
   3     <plugins workers="2">
   4         <plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
   5     </plugins>
   6     <handlers default="handlers">
   7         <handler id="handler0" tags="handlers"/>
   8         <handler id="handler1" tags="handlers"/>
   9     </handlers>
  10     <destinations default="gridengine">
  11         <destination id="gridengine" runner="gridengine"/>
  12     </destinations>
  13     <limits>
  14         <limit type="registered_user_concurrent_jobs">2</limit>
  15         <limit type="unregistered_user_concurrent_jobs">1</limit>
  16         <limit type="job_walltime">24:00:00</limit>
  17     </limits>
  18 </job_conf>

This VM comes preconfigured with Torque, Grid Engine, and SLURM - Galaxy can submit jobs to any of these as well as LSF, Condor, etc... but the above configuration will just target the VM's default - Grid Engine.

Start a Galaxy server to complete first run setup

   1 gxprod@gcc2014:~/galaxy-dist$ sh run.sh
   2 Initializing datatypes_conf.xml from datatypes_conf.xml.sample
   3   ...
   4 serving on http://127.0.0.1:8080
   5 ^C
   6   ...
   7 gxprod@gcc2014:~/galaxy-dist$ logout
   8 galaxy@gcc2014:~$ 

Install nginx, uWSGI, and supervisord

   1 galaxy@gcc2014:~/galaxy-dist$ sudo add-apt-repository ppa:natefoo/bioit2014
   2  Provides a rebuilt nginx-extras with the upload module for the workshop @
   3  Bio-IT World Expo 2014
   4  More info: https://launchpad.net/~natefoo/+archive/bioit2014
   5 Press [ENTER] to continue or ctrl-c to cancel adding it
   6 
   7 gpg: keyring `/tmp/tmp71rhd5g3/secring.gpg' created
   8 gpg: keyring `/tmp/tmp71rhd5g3/pubring.gpg' created
   9 gpg: requesting key 12788738 from hkp server keyserver.ubuntu.com
  10 gpg: /tmp/tmp71rhd5g3/trustdb.gpg: trustdb created
  11 gpg: key 12788738: public key "Launchpad PPA for Nate Coraor" imported
  12 gpg: Total number processed: 1
  13 gpg:               imported: 1  (RSA: 1)
  14 OK
  15 galaxy@gcc2014:~/galaxy-dist$ sudo apt-get update
  16   ...
  17 Fetched 141 kB in 4s (34.0 kB/s)
  18 Reading package lists... Done
  19 galaxy@gcc2014:~/galaxy-dist$ sudo apt-get install nginx-extras uwsgi uwsgi-plugin-python supervisor
  20   ...
  21 After this operation, 10.4 MB of additional disk space will be used.
  22 Do you want to continue? [Y/n]
  23 Get:1 http://ppa.launchpad.net/natefoo/bioit2014/ubuntu/ trusty/main nginx-common all 1.4.6-1ubuntu3ppa1 [81.5 kB]
  24 Get:2 http://ppa.launchpad.net/natefoo/bioit2014/ubuntu/ trusty/main nginx-extras amd64 1.4.6-1ubuntu3ppa1 [570 kB]
  25   ...
  26 galaxy@gcc2014:~/galaxy-dist$ sudo /etc/init.d/nginx stop
  27 galaxy@gcc2014:~/galaxy-dist$ sudo update-rc.d -f nginx remove
  28  Removing any system startup links for /etc/init.d/nginx ...
  29    /etc/rc0.d/K20nginx
  30    /etc/rc1.d/K20nginx
  31    /etc/rc2.d/S20nginx
  32    /etc/rc3.d/S20nginx
  33    /etc/rc4.d/S20nginx
  34    /etc/rc5.d/S20nginx
  35    /etc/rc6.d/K20nginx
  36 galaxy@gcc2014:~/galaxy-dist$ sudo update-rc.d -f uwsgi remove
  37  Removing any system startup links for /etc/init.d/uwsgi ...
  38    /etc/rc0.d/K20uwsgi
  39    /etc/rc1.d/K20uwsgi
  40    /etc/rc2.d/S20uwsgi
  41    /etc/rc3.d/S20uwsgi
  42    /etc/rc4.d/S20uwsgi
  43    /etc/rc5.d/S20uwsgi
  44    /etc/rc6.d/K20uwsgi
  45 galaxy@gcc2014:~/galaxy-dist$ 

Configure nginx

   1 galaxy@gcc2014:~$ cd /etc/nginx/
   2 galaxy@gcc2014:/etc/nginx$ sudo vi nginx.conf 
   3   ...
   4   user gxprod;
   5   daemon off;
   6   http {
   7       gzip_vary on;
   8       gzip_proxied any;
   9       gzip_comp_level 6;
  10       gzip_buffers 16 8k;
  11       gzip_http_version 1.1;
  12       gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
  13   }
  14   ...
  15 ubuntu@bioit:/etc/nginx$ cd sites-available
  16 ubuntu@bioit:/etc/nginx/sites-available$ sudo vi galaxy

In the editor, paste:

   1 client_max_body_size 50g;
   2 uwsgi_read_timeout 300;
   3 
   4 server {
   5     listen 80 default_server;
   6     server_name  bioit.galaxyproject.org;
   7 
   8     # pass to uWSGI by default
   9     location / {
  10         uwsgi_pass 127.0.0.1:4001;
  11         include uwsgi_params;
  12     }
  13 
  14     # serve static content
  15     location /static {
  16         alias /home/galaxy/galaxy-dist/static;
  17         gzip on;
  18         gzip_types text/plain text/xml text/javascript text/css application/x-javascript;
  19         expires 24h;
  20     }
  21     location /static/style {
  22         alias /home/galaxy/galaxy-dist/static/style/blue;
  23         gzip on;
  24         gzip_types text/plain text/xml text/javascript text/css application/x-javascript;
  25         expires 24h;
  26     }
  27     location /static/scripts {
  28         alias /home/galaxy/galaxy-dist/static/scripts/packed;
  29         gzip on;
  30         gzip_types text/plain text/javascript application/x-javascript;
  31         expires 24h;
  32     }
  33     location ~ ^/plugins/visualizations/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
  34         alias /home/galaxy/galaxy-dist/config/plugins/visualizations/$vis_name/static/$static_file;
  35     }
  36 
  37     # delegated downloads
  38     location /_x_accel_redirect {
  39         internal;
  40         alias /;
  41     }
  42 
  43     # delegated uploads
  44     location /_upload {
  45         upload_store /home/galaxy/uploads;
  46         upload_store_access user:rw;
  47         upload_pass_form_field "";
  48         upload_set_form_field "__${upload_field_name}__is_composite" "true";
  49         upload_set_form_field "__${upload_field_name}__keys" "name path";
  50         upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
  51         upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
  52         upload_pass_args on;
  53         upload_pass /_upload_done;
  54     }
  55     location /_upload_done {
  56         set $dst /api/tools;
  57         if ($args ~ nginx_redir=([^&]+)) {
  58             set $dst $1;
  59         }
  60         rewrite "" $dst;
  61     }
  62 }

   1 galaxy@gcc2014:/etc/nginx/sites-enabled$ sudo rm default 
   2 galaxy@gcc2014:/etc/nginx/sites-enabled$ sudo ln -fs ../sites-available/galaxy
   3 galaxy@gcc2014:/etc/nginx/sites-enabled$ 

Configure supervisord

   1 ubuntu@bioit:~$ cd /etc/supervisor/conf.d
   2 ubuntu@bioit:/etc/supervisor/conf.d$ sudo vi galaxy.conf

In the editor, paste:

   1 [program:nginx]
   2 command         = /usr/sbin/nginx
   3 directory       = /
   4 umask           = 022
   5 autostart       = true
   6 autorestart     = unexpected
   7 startsecs       = 5
   8 exitcodes       = 0
   9 user            = root
  10 
  11 [program:galaxy_uwsgi]
  12 command         = /usr/bin/uwsgi --plugin python --ini-paste /home/galaxy/galaxy-dist/universe_wsgi.ini
  13 directory       = /home/galaxy/galaxy-dist
  14 umask           = 022
  15 autostart       = true
  16 autorestart     = true
  17 startsecs       = 10
  18 user            = galaxy
  19 environment     = PATH=/home/galaxy/venv:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHON_EGG_CACHE=/home/galaxy/.python-eggs,PYTHONPATH=/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg
  20 numprocs        = 1
  21 stopsignal      = INT
  22 
  23 [program:handler]
  24 command         = /home/galaxy/venv/bin/python ./scripts/paster.py serve universe_wsgi.ini --server-name=handler%(process_num)s --pid-file=/home/galaxy/handler%(process_num)s.pid --log-file=/home/galaxy/handler%(process_num)s.log
  25 directory       = /home/galaxy/galaxy-dist
  26 process_name    = handler%(process_num)s
  27 numprocs        = 2
  28 umask           = 022
  29 autostart       = true
  30 autorestart     = true
  31 startsecs       = 15
  32 user            = galaxy
  33 environment     = PYTHON_EGG_CACHE=/home/galaxy/.python-eggs,DRMAA_LIBRARY_PATH=/usr/lib/gridengine-drmaa/lib/libdrmaa.so.1.0,SGE_ROOT=/var/lib/gridengine
  34 
  35 [group:galaxy]
  36 programs = handler

Start Galaxy and nginx

   1 ubuntu@bioit:~$ sudo supervisorctl update
   2 galaxy: added process group
   3 galaxy_uwsgi: added process group
   4 nginx: added process group
   5 ubuntu@bioit:~$ sudo supervisorctl status
   6 galaxy:handler0                  STARTING
   7 galaxy:handler1                  STARTING
   8 galaxy_uwsgi                     STARTING
   9 nginx                            STARTING
  10 

You can now visit your Galaxy server at:

VM Galaxy Instances

bioit0

bioit1

bioit2

bioit3

bioit4

bioit5

bioit6

bioit7

bioit8

bioit9

bioit10

bioit11

bioit12

bioit13

bioit14

bioit15

bioit16

bioit17

bioit18

bioit19

bioit20

bioit21

bioit22

bioit23

bioit24

bioit25

bioit26

bioit27

bioit28

bioit29

bioit30

bioit31

bioit32

bioit33

bioit34

bioit35

bioit36

bioit37

bioit38

bioit39

References

Transcripts

Adding local data by hand

   1 ubuntu@bioit:~$ mkdir -p ~/local_data/sacCer2/seq/work
   2 ubuntu@bioit:~$ cd ~/local_data/sacCer2/seq/work
   3 ubuntu@bioit:~/local_data/sacCer2/seq/work$ rsync -vz rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/chromFa.tar.gz .
   4 chromFa.tar.gz
   5 
   6 sent 51 bytes  received 3,824,563 bytes  1,092,746.86 bytes/sec
   7 total size is 3,823,174  speedup is 1.00
   8 ubuntu@bioit:~/local_data/sacCer2/seq/work$ tar zxvf chromFa.tar.gz
   9 2micron.fa
  10 chrI.fa
  11 chrII.fa
  12 chrIII.fa
  13 chrIV.fa
  14 chrIX.fa
  15 chrM.fa
  16 chrV.fa
  17 chrVI.fa
  18 chrVII.fa
  19 chrVIII.fa
  20 chrX.fa
  21 chrXI.fa
  22 chrXII.fa
  23 chrXIII.fa
  24 chrXIV.fa
  25 chrXV.fa
  26 chrXVI.fa
  27 ubuntu@bioit:~/local_data/sacCer2/seq/work$ cat *.fa >../sacCer2.fa
  28 ubuntu@bioit:~/local_data/sacCer2/seq/work$ cd ../..
  29 ubuntu@bioit:~/local_data/sacCer2$ mkdir bwa_index
  30 ubuntu@bioit:~/local_data/sacCer2$ cd bwa_index
  31 ubuntu@bioit:~/local_data/sacCer2/bwa_index$ ~/tool_deps/bwa/0.5.9/devteam/package_bwa_0_5_9/ec2595e4d313/bin/bwa index -a bwtsw sacCer2.fa
  32 [bwa_index] Pack FASTA... 0.18 sec
  33 [bwa_index] Reverse the packed sequence... 0.06 sec
  34 [bwa_index] Construct BWT for the packed sequence...
  35 [BWTIncConstructFromPacked] 10 iterations done. 2968163 characters processed.
  36 [BWTIncConstructFromPacked] 20 iterations done. 5189523 characters processed.
  37 [BWTIncConstructFromPacked] 30 iterations done. 6938035 characters processed.
  38 [BWTIncConstructFromPacked] 40 iterations done. 8313523 characters processed.
  39 [BWTIncConstructFromPacked] 50 iterations done. 9394739 characters processed.
  40 [BWTIncConstructFromPacked] 60 iterations done. 10243827 characters processed.
  41 [BWTIncConstructFromPacked] 70 iterations done. 10909811 characters processed.
  42 [BWTIncConstructFromPacked] 80 iterations done. 11431331 characters processed.
  43 [BWTIncConstructFromPacked] 90 iterations done. 11838867 characters processed.
  44 [BWTIncConstructFromPacked] 100 iterations done. 12156547 characters processed.
  45 [bwt_gen] Finished constructing BWT in 101 iterations.
  46 [bwa_index] 3.30 seconds elapse.
  47 [bwa_index] Construct BWT for the reverse packed sequence...
  48 [BWTIncConstructFromPacked] 10 iterations done. 2968163 characters processed.
  49 [BWTIncConstructFromPacked] 20 iterations done. 5189523 characters processed.
  50 [BWTIncConstructFromPacked] 30 iterations done. 6938035 characters processed.
  51 [BWTIncConstructFromPacked] 40 iterations done. 8313523 characters processed.
  52 [BWTIncConstructFromPacked] 50 iterations done. 9394739 characters processed.
  53 [BWTIncConstructFromPacked] 60 iterations done. 10243827 characters processed.
  54 [BWTIncConstructFromPacked] 70 iterations done. 10909811 characters processed.
  55 [BWTIncConstructFromPacked] 80 iterations done. 11431331 characters processed.
  56 [BWTIncConstructFromPacked] 90 iterations done. 11838867 characters processed.
  57 [BWTIncConstructFromPacked] 100 iterations done. 12156547 characters processed.
  58 [bwt_gen] Finished constructing BWT in 101 iterations.
  59 [bwa_index] 3.41 seconds elapse.
  60 [bwa_index] Update BWT... 0.08 sec
  61 [bwa_index] Update reverse BWT... 0.07 sec
  62 [bwa_index] Construct SA from BWT and Occ... 1.03 sec
  63 [bwa_index] Construct SA from reverse BWT and Occ... 1.02 sec
  64 ubuntu@bioit:~/local_data/sacCer2/bwa_index$ cd ~/galaxy-dist/tool-data
  65 ubuntu@bioit:~/galaxy-dist/tool-data$ vim bwa_index.loc
  66   ...
  67   sacCer2byhand   sacCer2 S. cerevisiae June 2008 (index by hand) /home/ubuntu/local_data/sacCer2/bwa_index/sacCer2.fa
  68   ...
  69 ubuntu@bioit:~/galaxy-dist/tool-data$ cd ..
  70 ubuntu@bioit:~/galaxy-dist$ vim tool_data_table_conf.xml
  71   ...
  72   <table name="bwa_indexes" comment_char="#">
  73       <columns>value, dbkey, name, path</columns>
  74       <file path="tool-data/bwa_index.loc" />
  75   </table>
  76   ...
  77 ubuntu@bioit:~/galaxy-dist$ sh run.sh
  78   ...
  79