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Proxy error while testing FASTX tools?
by Sebastian Schaaf 25 Jun '13

25 Jun '13

Hi all, I've got a relatively fresh installed Galaxy instance running within a locked network, where internet access is allowed only via a proxy. So far, so simple; indeed I get internet access via a terminal (e.g. calling Google with lynx), also wget and mercurial have the chance to access target URL's. The variables $http_proxy, $https_proxy and $ftp_proxy are set. My problem occurs when I try to execute the automatic tests (using 'run_functional_tests.sh') for the FASTX toolbox, described here right at the end: http://hannonlab.cshl.edu/fastx_toolkit/download.html The calls of the scripts generally end up in an error block of the following scheme: ##### functional_tests.py DEBUG 2013-06-25 14:15:40,406 Attempting to serve app on randomly chosen port: 8720 functional_tests.py INFO 2013-06-25 14:15:40,468 Embedded web server started base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.text base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.tabular base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.xml functional_tests.py INFO 2013-06-25 14:15:40,506 Functional tests will be run against localhost:8720 nose.plugins.manager DEBUG 2013-06-25 14:15:40,518 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTes tDiff nose.plugins.manager DEBUG 2013-06-25 14:15:40,520 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML Uncollapse ( cshl_fastx_uncollapser ) > Test-1 ... ERROR ====================================================================== ERROR: Uncollapse ( cshl_fastx_uncollapser ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 53, in setUp self.home() File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 1141, in home self.visit_url( self.url ) File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 1324, in visit_url tc.code( 200 ) File "/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 133, in code should_be)) TwillAssertionError: code is 403 != 200 ---------------------------------------------------------------------- Ran 1 test in 0.011s FAILED (errors=1) ##### For me it reads like there is problem while testing to call the URL in self.url, which resolves to 'localhost:9441'. URL and port are drawn from the environment in the script ".../galaxy-dist/test/base/twilltestcase.py": ##### class TwillTestCase( unittest.TestCase ): def setUp( self ): [...] self.host = os.environ.get( 'GALAXY_TEST_HOST' ) self.port = os.environ.get( 'GALAXY_TEST_PORT ) self.url = "http://%s:%s" % ( self.host, self.port ) [...] ##### I could neither observe any process listening to port 9441 during the test script execution, nor any of the text files within the galaxy root dir contained '9441' as part of a configuration option. Finally I'm a bit confused what that means to me, beyond just not to be able to use the test suite. Anyone an idea what could and/or should be fixed or checked? Thanks in advance, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich

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How to enable auto option for newly added file formats
by shashi shekhar 25 Jun '13

25 Jun '13

Hi, I want to enable option auto option for some format ..how will i proceed . I have alreadu added the format in galaxy ., which works without auto option. Regards shashi

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account avatar
by Philipe Moncuquet 24 Jun '13

24 Jun '13

Hi, We are running a local instance of Galaxy behind firewall. How can one modify the picture associated with is galaxy account in the configuration ? Regards, Philippe

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GATK tools not showing up in cloudman Galaxy installation
by Marco Ocana 24 Jun '13

24 Jun '13

Hi, When starting up Galaxy from Cloudman and updating the latest version from repository, most of the GATK tools do not show up in the tool bar. I have attached the log file. There are other errors in the log file, but I have pasted what I believe the relavant section of the log. Any pointers on how to fix the problem would be appreciated. Thanks Marco Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,272 Error reading tool from path: gatk/indel_realigner.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,281 Error reading tool from path: gatk/count_covariates.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,290 Error reading tool from path: gatk/table_recalibration.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' galaxy.tools ERROR 2013-06-20 17:54:00,323 Error reading tool from path: gatk/unified_genotyper.xml Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 396, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 515, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 855, in __init__ self.parse( root, guid=guid ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1028, in parse self.parse_inputs( root ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1112, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1516, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1583, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1539, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line 1621, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 1361, in __init__ ToolParameter.__init__( self, tool, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 25, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'

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[GSoC2013] Week 1 Accomplishments and Week 2 Plans
by Saket Choudhary 24 Jun '13

24 Jun '13

Hi Everyone, Just wrote a blog post for my Week1 tasks and Week 2 to-dos: http://galaxy-gsoc2013.blogspot.in/2013/06/week-1-accomplishments-and-week-… I am maintaining a work log in this doc : https://docs.google.com/document/d/1VCKCpKW6C_Tt1DYWi43GAN_Jo-nebkkj8Ctq7WL… If you have any suggestions for the VCF4.1 issue or otherwise. please do let me know. Thanks Saket Choudhary Undergraduate Dept. of Chemical Engineering IIT Bombay

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Re: [galaxy-dev] [galaxy-user] Problems when downloading a local galaxy tool (old version)
by Dannon Baker 23 Jun '13

23 Jun '13

Hsiong, Could you try 'hg clone --verbose --debug https://bitbucket.org/galaxy/galaxy-dist/' to see if we get more useful error output? If it passed the warning and went ahead and got all the changes then I'm not sure if that's an issue. Also, I'm swapping this thread to the galaxy-dev list, since it's about installing a local instance. -Dannon On Sun, Jun 23, 2013 at 1:15 AM, xiong <lynhsiong(a)hotmail.com> wrote: > ** > Dear friends: > > As a locally installed Genomic-hyperbrowser need a rather old > version of Galaxy, I runed the command "hg clone > https://bitbucket.org/galaxy/galaxy-dist/ -u 26920e20157f galaxy-dist-hb" > according to the website > http://hyperbrowser.uio.no/hb/static/download.html. However, the hg did > not download successfully, but reported > > "warning: bitbucket.org certificate with fingerprint > 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified > (check hostfingerprints or web.cacerts config setting) > destination directory: galaxy-dist-hb > requesting all changes > adding changesets" > > and this information on the screen mainteined (at least half a day unless > I hit "ctrl+Z" and kill the job) without any other errors (still in the > destination directory it generated a nearly empty dir > "galaxy-dist-hb" containing a filefold named ".hg”——one "store" filefold > and several small files included). My mercurial version is 2.6, and I use > Xshell to reach CentOS Server. > > Actually, even I downloaded the latest version of galaxy (hg clone > https://bitbucket.org/galaxy/galaxy-dist/) it also reported the same > information on the screen. > On the other hand, I can get the latest tarballs of galaxy, but > it can not be updated to an old version. > > Please give me some clues about problems above, and any ideas to get > tarballs for an old version? > > Thanks in advance! > > Hsiong > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > 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/ >

1 0

Profile loss
by Marley Yeong 22 Jun '13

22 Jun '13

Dear sir or madam, It seems my profile has been deleted, before galaxy went offline (about two weeks ago) I made a profile with the email address: marleyyeong(a)live.nl.I keep getting the "no such user" error. And I'm pretty sure the login information is typed correctly.It stored a school project, so any help would be greatly appreciated. Thanks in advance, Marley Yeong

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Re: [galaxy-dev] Portable tool identifiers in workflows
by Peter Cock 22 Jun '13

22 Jun '13

On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Peter, > > Unfortunately, workflows are currently not very compatible with > the tool shed - there is a Trello card that details the issues here: > > https://trello.com/card/workflow-issues/506338ce32ae458f6d15e4b3/692 > Thanks Greg - I see that Trello card is "in progress", but it covers quite a broad range of issues. >> So, does Galaxy handle old fashioned tool identifiers and the >> newer toolshed-tool-identifiers gracefully in a situation like this? > > Unfortunately this does not currently work ... > >> Do I need to update the *.ga files to use toolshed-tool-ids? If >> I did that, would it break the workflow on any Galaxy instance >> (like ours) where the tools were installed manually? > > Yes, you would currently need to update the workflows to use > toolshed-tool-ids, and your statement regarding the workflow > not working with older tools is correct. So in the short term the best thing to do is to edit these workflows as posted on the Tool Shed (easy enough as the *.ga files are plain text) to replace the tool identifiers? What would be the easiest way to work out the desired id form from a tool repository page? Other than reinstalling the tools locally but from the Tool Shed this time? ;) Thanks, Peter

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Re: [galaxy-dev] ProFTPD integration with Galaxy
by Perez, Ricardo 21 Jun '13

21 Jun '13

Hi Mr. Tobias, We are having a similar problem. It seems that when the galaxy code was updates, new created/updated passwords are using a different encryption mode. This new mode, PBKDF2 SHA256 is NOT supported by proftpd 1.3.4d that you see to be using. We had to compile proftpd from source since version 1.3.5rc3 does support this encryption. Now in the password PBKDF2$sha256$10000$8h/4HmD1Eu6NTc7F$Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh I was able to deduce the following by reading the code from git hub "password.py". The encrypted password is acually Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh where the salt is 8h/4HmD1Eu6NTc7F using PBKDF2 SHA256 with an illiteration value of 10000. The most importnat part is that the salt, is right there, from character 21 to 36. With the newly compiled proftpd, I have the following configuration at proftpd.conf: # This is a basic ProFTPD configuration file (rename it to # 'proftpd.conf' for actual use. It establishes a single server # and a single anonymous login. It assumes that you have a user/group # "nobody" and "ftp" for normal operation and anon. ServerName "Genomics01 ProFTPd" ServerType standalone DefaultServer on DeferWelcome off UseIPv6 on IdentLookups off MultilineRFC2228 on ShowSymlinks on ModulePath /usr/local/galaxy/downloads/proftpd-1.3.5rc3/modules/ LoadModule mod_sql.c LoadModule mod_sql_postgres.c LoadModule mod_sql_passwd.c <IfModule mod_sql.c> SQLBackend postgres SQLEngine on SQLAuthenticate users SQLAuthTypes SHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 1000 24 #SQLPasswordSaltFile /path/to/file SQLConnectInfo galaxydb@localhost:5432 ftpuser mypassword SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email,password,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLPasswordUserSalt sql:/GetUserSalt SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) END) AS salt FROM galaxy_user WHERE email='%U'" </IfModule> SQLDefaultGID 1002 SQLDefaultUID 1002 TimeoutNoTransfer 600 TimeoutStalled 600 TimeoutIdle 1200 DisplayLogin welcome.msg DisplayChdir .message true ListOptions "-l" DenyFilter \*.*/ # Use this to jail all users in their homes DefaultRoot ~ CreateHome on dirmode 700 AllowOverwrite on AllowStoreRestart on SQLPasswordEngine on SQLPasswordEncoding hex PassivePorts 30000 40000 # Port 21 is the standard FTP port. Port 21 # Don't use IPv6 support by default. # 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 galaxy Group galaxy # To cause every FTP user to be "jailed" (chrooted) into their home # directory, uncomment this line. #DefaultRoot ~ # Normally, we want files to be overwriteable. AllowOverwrite on #AuthOrder mod_sql.c # Bar use of SITE CHMOD by default #<Limit SITE_CHMOD> # DenyAll #</Limit> Include /etc/proftpd/conf.d/ With the configuration above, I can still connect to users that have SHA1 passwords, but I think I need a little more tweeking to get it to work with the new passwords. Best, --Ricardo Perez

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Installation of 20130603 Galaxy image with MySQL fails
by Linda Cham 21 Jun '13

21 Jun '13

Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, "BLOB/TEXT column 'slug' used in key specification without a key length") 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql> CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 When trying to run.sh again after the CREATE INDEX, will get this error: File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get ( '__file__', None ), self.config.database_engine_options, app=self ) File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py", line 107, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '29' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. So try to run the "sh manage_db.sh upgrade' now will get this error: $ sh manage_db.sh upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 13, in <module> from migrate.versioning.shell import main File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 12, in <module> from migrate.versioning import api File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 33, in <module> from migrate.versioning import (repository, schema, version, File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 13, in <module> from migrate.versioning import version, pathed, cfgparse File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 10, in <module> from migrate.versioning import pathed, script File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py", line 11, in <module> from migrate.versioning.util import KeyedInstance File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 7, in <module> from decorator import decorator ImportError: No module named decorator In some searches, there were tips of deleting the eggs directory and rerun run.sh or use a python env. Neither option worked. Was not able to find anything meaningful about the decorator error. Note:, I was able to get Galaxy up with MySQL using the Galaxy 788cd3d06541 image on a different node. So I am thinking maybe it is the new 20130603 image that is giving me issues? Commands used to get Galaxy up: Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1] python version [2.6.6] Grant ALL PRIVILEGES galaxy_db.* TO galaxy_user on localhostname with PWD Images tested: *Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image Did not run the hg update command. [This worked] *hg clone stable of newest image [Failed] Update the universe_wsg.ini with the port, host, database_connection to mysql Ran run.sh Thanks. Linda

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