galaxy-dev April 2016

galaxy-dev@lists.galaxyproject.org

47 participants
55 discussions

ERROR: PIP is not a legl parament of an Ansible Play
by William Ge 21 Apr '16

21 Apr '16

Hi, all, Sorry to bother you again. I am trying to install tools using the script. I have downloaded the playbook, but stuck here: [galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx ERROR: pip is not a legal parameter of an Ansible Play I did not find anything related on the Galaxy search either. Any help will be appreciated. The web Admin interface only allows tool installation one by one. I wish it allows batch installation there. Thanks, Bill

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Main Toolshed Account password reset
by Oksana Korol 21 Apr '16

21 Apr '16

Sorry for the previous email's subject line. Re-sending the questions with the proper subject. Hi, Who is the administrator on Galaxy Main Toolshed ( https://toolshed.g2.bx.psu.edu)? I'm trying to re-set a password for the work Galaxy toolshed account, but I think that the email is blocked by our firewall. Who can I contact to resolve this issue? Thanks! -- :: Oksana Korol

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Re: [galaxy-dev] galaxy-dev Digest, Vol 118, Issue 18
by Oksana Korol 21 Apr '16

21 Apr '16

Hi, Who is the administrator on Galaxy Main Toolshed ( https://toolshed.g2.bx.psu.edu)? I'm trying to re-set a password for the work Galaxy toolshed account, but I think that the email is blocked by our firewall. Who can I contact to resolve this issue? Thanks! Oksana Korol

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GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile Devices; and Tools, Tools, Tools!
by Hotz, Hans-Rudolf 21 Apr '16

21 Apr '16

Hello all, The next <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_04_21> GalaxyAdmins<https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_04_21> online meetup<https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_04_21> is this Thursday, April 21 at 5PM CET (see your local time<http://bit.ly/1RpBa8e> to know when to connect): The featured topics are: The Galaxy Portal: Accessing Galaxy from Mobile Devices<http://bioinformatics.oxfordjournals.org/content/early/2016/02/17/bioinform…> Ivar Grytten<http://www.mn.uio.no/ifi/english/people/aca/ivargry/> and Geir Kjetil Sandve<http://www.mn.uio.no/ifi/english/people/aca/geirksa/>, University of Oslo<http://www.uio.no/> Tool Development Developments John Chilton<https://wiki.galaxyproject.org/JohnChilton>, Penn State University<http://psu.edu/> The meetup will use the same Adobe Connect technology used on previous calls. The 'Meeting Room Link' will be provided on the wiki page in time. It takes a couple of minutes to connect, so you are encouraged to start connecting a few minutes early. See http://bit.ly/gxyadm201604 for full details. Thanks, Dave C and Hans-Rudolf ---- GalaxyAdmins<https://wiki.galaxyproject.org/Community/GalaxyAdmins> is a discussion group for Galaxy community members who are responsible for Galaxy installations.

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FTP Authentication Against Postgres Database with PBKDF2
by Joseph Brent Greer 20 Apr '16

20 Apr '16

Hi All, We're having problems setting up ftp and authenticating against the postgres database. We've reviewed these pages and a few others: Galaxy Page: https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP Peter Briggs Blog Post: http://galacticengineer.blogspot.co.uk/2015/02/ftp-upload-to-galaxy-using-p… Ricardo Perez's Galaxy Developers thread that Peter referenced: http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295… When we run proftpd in debug mode we get similar output to the one in Ricardo's thread: Ricardo's command line output: login002 proftpd[987] login002 (10.28.56.101[10.28.56.101]): mod_sql_passwd/0.4: expected 'PBKDF2$sha256$10000$8h/4HmD1Eu6NTc7F$Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh', got 'cc0ef515d684386aaa500bf6499d9f512dfb332c' Our output: 2016-04-20 10:53:42,597 pcegalaxy proftpd[18649] pcegalaxy.ci.northwestern.edu (lagunitas.kelleher.northwestern.edu[129.105.112.217]): mod_sql_passwd/0.7: expected 'NMmACzgvs8Oh+BCnSw+2GFxpYl7cLiQu', got 'g3L81voHwAEh8y0B9qBImZycWgS0w4Z4' >From looking at the galaxy_user table, it seems like proftpd is finding the correct password information (password in table: PBKDF2$sha256$10000$kgyVpO6N2rWAbeX6$NMmACzgvs8Oh+BCnSw+2GFxpYl7cLiQu). The last post from that thread mentions back-channel advice that was helpful. Maybe we need the same advice ? In case it's important we're using LDAP for our general user authentication. Here is our proftpd.conf: ServerName "Galaxy FTP File Upload" ServerType standalone DefaultServer on PidFile /opt/apps/proftpd/1.3.5/var/proftpd.pid # Port 21 is the standard FTP port. Port 21 # Don't use IPv6 support by default. UseIPv6 off # Umask 022 is a good standard umask to prevent new dirs and files # from being group and world writable. Umask 077 # To prevent DoS attacks, set the maximum number of child processes # to 30. If you need to allow more than 30 concurrent connections # at once, simply increase this value. Note that this ONLY works # in standalone mode, in inetd mode you should use an inetd server # that allows you to limit maximum number of processes per service # (such as xinetd). MaxInstances 30 # Set the user and group under which the server will run. User nobody Group nobody # To cause every FTP user to be "jailed" (chrooted) into their home # directory, uncomment this line. DefaultRoot ~ # Automatically create home directory if it doesn't exist CreateHome on dirmode 700 # Allow users to overwrite their files AllowOverwrite on # Allow users to resume interrupted uploads AllowStoreRestart on # Bar use of SITE CHMOD by default <Limit SITE_CHMOD> DenyAll </Limit> # Bar use of RETR (download) since this is not a public file drop <Limit RETR> DenyAll </Limit> # Do not authenticate against real (system) users AuthPAM off ## Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1 SQLPasswordEngine on ## Set this if Galaxy user UID and/or GID are less than 999 SQLMinID 400 ## Configuration that handles PBKDF2 encryption ## Set up mod_sql to authenticate against the Galaxy database SQLEngine on SQLBackend postgres SQLConnectInfo galaxy_db@localhost:5432 <USERNAME> <PASSWORD> SQLAuthTypes PBKDF2 SQLPasswordPBKDF2 SHA256 10000 24 SQLPasswordEncoding base64 SQLAuthenticate users ## For PBKDF2 authentication SQLPasswordUserSalt sql:/GetUserSalt ## Define a custom query for lookup that returns a passwd-like entry for PBKFD2 ## UID and GID should match your Galaxy user. SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,400,400,'/share/PCEitAdmin/Galaxy/external_users/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" ## Define custom query to fetch the password salt SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U'" Any advice would be great. Thanks, Joe Greer Northwestern University

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galaxy running problem
by V.Freire-Beneitez 20 Apr '16

20 Apr '16

Dear Sir or Madam, Since yesterday I have been trying to run some RNA-sequencing analysis using the tools from galaxy, but it seems that it is frozen not even sending to queue the runnings and the tophats are not working. The webpage says that it is being updated and there could be some problems. I would like to ask you if more people is encountering this issue and if there is any way I could solve it. Thanks a lot for your time and help Regards, Veronica

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set_metadata in galaxy_XXX.sh script
by Laure QUINTRIC 20 Apr '16

20 Apr '16

Hi there (sorry for all theses questions), when I execute a job with remote user drmaa configuration on our pbs cluster, I see in the job working directory the script the galaxy_XXX.sh which set the galaxy virtual env and execute set_metadata.py after tool_script.sh completion but I get this in cluster error output : python: /lib64/libz.so.1: no version information available (required by python) Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] Traceback (most recent call last): File "galaxy/database/job_working_directory/002/2824/set_metadata_tkCRRk.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "galaxy/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 15, in <module> import json ImportError: No module named json The tool is execution is ok but the metadata script failed, but as that script is executed on the cluster and not on galaxy server, (I think) the virtual env is not properly set. Is there a way to remove set_metadata from galaxy_XXX.sh script as It was in v16.01 ? I don't really understand what to set in galaxy.ini (I tried to set retry_metadata_internally to True and then False but I get the same result). Regards, Laure

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galaxy v16.04 drmaa remote user and local upload
by Laure QUINTRIC 20 Apr '16

20 Apr '16

Hi there, I read this thread : http://dev.list.galaxyproject.org/external-chown-script-py-and-the-local-jo… (sorry not to answer in this thread but I'm new to the list). I'm using galaxy 16.04 (and the corrected files should be included as it is merge in 16.04: https://github.com/galaxyproject/galaxy/pull/1688) with remote user drmaa job execution. I set the upload tool to be executed on local runner in job_conf.xml , I kept the external_chown_script set in galaxy.ini and still get the permission denied error while uploading a file. How should it be configured in galaxy.ini and job_conf.xml to upload files locally and other jobs with drmaa with external_chown_script.py only executed for drmaa tools and not for local ones ? Do you have a working example ? Thanks a lot. Laure

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remote user CAS invalide session
by Laure QUINTRIC 20 Apr '16

20 Apr '16

Hi galaxy users, I just installed version 16.04 of galaxy. I can connect to galaxy with remote user through CAS authentification but my session is invalidated, I get this message in the history : An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists. Details <javascript:void(0)> In paster.log, I can see this : galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged in as 'toto(a)company.fr' externally, but has a cookie as 'toto' invalidating session and just after I can see : galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged in as 'toto' externally, but has a cookie as 'toto(a)company.fr' invalidating session It seems that variables remote_user_email and galaxy_session.user.email ( in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and then set to login only... so the user login is not always the user email address. In the config/galaxy.ini I set remote_user_maildomain = company.fr remote_user_header = HTTP_CAS_UID Can you tell me how to go through this ? I did not have this problem in v16.01. Best regards

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Question: Cannot start local Galaxy after upgrade to v16.01
by D K 19 Apr '16

19 Apr '16

Hi Galaxy Devs, I posted this question on biostars but didn't get an answer so I'll try here: I just tried upgrading my local instance of Galaxy from 15.10 to 16.01. When I start it up I get an error. Does anyone have any suggestions? galaxy@galaxy galaxy$ sh run.sh Activating virtualenv at .venv DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6 Ignoring indexes: https://pypi.python.org/simple /opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwar…. InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in ./.venv/lib/python2.6/site-packages DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6 Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line 69)) Requirement already satisfied (use --upgrade to upgrade): importlib in ./.venv/lib/python2.6/site-packages (from kombu==3.0.30->-r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): ordereddict in ./.venv/lib/python2.6/site-packages (from kombu==3.0.30->-r requirements.txt (line 40)) You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6 Requirement already satisfied (use --upgrade to upgrade): psycopg2==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 1)) Requirement already satisfied (use --upgrade to upgrade): importlib==1.0.3 in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 2)) Requirement already satisfied (use --upgrade to upgrade): ordereddict==1.1 in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 3)) Requirement already satisfied (use --upgrade to upgrade): drmaa in ./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 4)) You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Unsetting $PYTHONPATH Activating virtualenv at .venv Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 637, in command server = loadserver(server_spec, name=server_name, relative_to=base, global_conf=vars) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 303, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 502, in get_context section) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 524, in _context_from_use object_type, name=use, global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 454, in get_context global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 376, in _loadegg return loader.get_context(object_type, name, global_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 668, in get_context object_type, name=name) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 688, in find_egg_entry_point pkg_resources.require(self.spec) File "/opt/galaxy/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/opt/galaxy/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: Paste

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galaxy-dev April 2016