August 2012 - galaxy-dev - lists.galaxyproject.org

EBI SRA download: connection time out
by Joachim Jacob 09 Aug '12

09 Aug '12

Hi all, I do not succeed in downloading data from SRA. For every dataset I use (from smaller one to bigger ones) I get this error, after running for a few minutes. The remote data source application may be off line, please try again later. Error: [Errno ftp error] [Errno 110] Connection timed out Any idea? cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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TopHat for paired end
by suzan katie 09 Aug '12

09 Aug '12

Hello, I am trying to run TopHat for paired end and this is my first time using Galaxy and TopHat and I have a doubt regarding what to mention in Mean Inner Distance between Mate Pairs:The default value is 20. Should I leave the value or should I be changing the value. What is Mean Inner Distance between Mate Pairs:? Thanks

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Bowtie .loc file with fasta.1.ebwt
by Robert Chase 09 Aug '12

09 Aug '12

Hello, I am trying to get the reference genomes to appear in our NGS tools. In my bowtie.loc file for instance I have the following line: hg18 /share/shared/data/genomes/hg18/bowtie/Homo_sapiens_assembly18.fasta.1.eb wt [galaxy@ tool-data]$ cd /share/shared/data/genomes/hg18/bowtie/ [galaxy]$ ls Homo_sapiens_assembly18.fasta.1.ebwt Homo_sapiens_assembly18.fasta.4.ebwt Homo_sapiens_assembly18.fasta.2.ebwt Homo_sapiens_assembly18.fasta.rev.1.ebwt Homo_sapiens_assembly18.fasta.3.ebwt Homo_sapiens_assembly18.fasta.rev.2.ebwt Do the files provided in the .loc file have to be fasta files? Where can these fasta files be obtained? -Rob

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Starting a Cloud Instance
by Jennifer Jackson 09 Aug '12

09 Aug '12

Re-Post to galaxy-dev On 8/7/12 3:01 AM, Mark Lindsay wrote: >> I wondered if you might be able to help. >> >> I have very little computing experience but have been trying to launch >> a cloud instance for the last 24 hrs. >> >> Initially I had problems launching the instance in Sahari i.e. it kept >> saying that it could not connect to the relevant page. >> >> When I have finally got top the CloudMan launch page it is giving the >> following message > > [Critical] Volume 'vol-dd6397db' is located in the wrong availability > zone for this instance. You MUST terminate this instance and start a new > one in zone 'us-east-1a' > >> despite the fact that I am sure I have started in zone 'us-east-1a. >> >> How important are the security codes and keys? >> >> BW >> >> Mark >> > ___________________________________________________________ > 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/ > -- Jennifer Jackson http://galaxyproject.org

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a problem with python version
by Rui Wang 09 Aug '12

09 Aug '12

Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message ************************************************************************* Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set ************************************************************************* However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Thanks, Rui

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Multi-level conditional output files
by John Patterson 09 Aug '12

09 Aug '12

Hello! The wiki entry on dealing with the <filter> tags is wonderful, but I seem to hit its limitations, unless someone has experience with multi-level conditionals in the input. For example in my XML, <conditional name="Build_Settings"> <param name="SettingsType" type="select" label="Settings to use"> <option value="preSet">Use Defaults</option> <option value="full">Full parameter list</option> </param> <when value="preSet" /> <when value="full"> <conditional name="Bam"> <param name="Bam_Output" type="select" label="Bam Output" > <option value="no">No</option> <option value="yes">Yes</option> </param> </conditional> </when> </conditional> The bam conditional sets an argument in my program to generate bam instead of sam (default) which is the reason for the conditional. There are two cases for sam output, when the option is preset, or when full parameters>bam_output == no. for this reason It wouldnt work to filter this on the bam_output boolean because it would evaluate to false if preset was chosen. I cannot do a simple <change format> for the same reason. Do the filter tags only support one boolean check? How would I actually get past the "settings" parameter and into the bam_output parameter?

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Odd (possible latency/race?) problems post-upgrade
by Fields, Christopher J 09 Aug '12

09 Aug '12

I'm seeing a possible latency issue or race condition when starting Galaxy after the latest hg upgrade (July 20) from galaxy-dist; the prior upgrade doesn't have this problem. We have small setup with one job manager/runner and two web front-ends for testing load balancing: …from universe_wsgi.ini: ------------------------------ [server:web0] use = egg:Paste#http port = 8080 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:web1] use = egg:Paste#http port = 8081 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:manager] use = egg:Paste#http port = 8079 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 ------------------------------ If I run: GALAXY_RUN_ALL=1 sh run.sh --daemon I will intermittently see the following in the paster log for any of the above services (example below is web1, but I have seen this for manager and web0 as well). The traceback and error is the same in all cases ('File exists: /home/a-m/galaxy/dist-database/tmp/work_tmp'): ------------------------------ galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-07-30 11:40:10,650 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-07-30 11:40:10,845 At database version 103 galaxy.tool_shed.migrate.check DEBUG 2012-07-30 11:40:10,940 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.migrate.check INFO 2012-07-30 11:40:10,986 At migrate_tools version 3 galaxy.model.custom_types DEBUG 2012-07-30 11:40:10,994 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/app.py", line 66, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line 47, in load_proprietary_datatypes installed_repository_dict = galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 1269, in load_installed_datatypes work_dir = make_tmp_directory() File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 1305, in make_tmp_directory os.makedirs( work_dir ) File "/usr/lib64/python2.6/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 17] File exists: '/home/a-m/galaxy/dist-database/tmp/work_tmp' Removing PID file web1.pid ------------------------------ I was also seeing this using separate runner/webapp ini files and 'run_multiple_processes.sh --daemon', but we decided to go ahead and migrate over to a unified universe_wsgi.ini file. Anyway, we found a workaround by rerunning 'GALAXY_RUN_ALL=1 sh run.sh --daemon' which skips any running services, but I'm curious whether anyone else has seen this and whether there is a fix (or maybe added config setting we are missing?) chris

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Error on database_connection statement in universe_wsgi.ini file
by Kenneth R. Auerbach 09 Aug '12

09 Aug '12

Hello, Galaxy runs fine 'out of the box' with the default universe_wsgi.ini initialization file. But when I change the "database_connection" statement to connect to my MySql database, I get the errors below. Can you please tell what the problem is? Thanks! -Wolf. Modification to universe_wsgi.ini file: ------------------------------------ #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock ------------------------------------- Then when I type "sh run.sh" I get this: --------- wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py", line 1997, in parse src ValueError: ("EntryPoint must be in 'name=module:attrs [extras]' format", 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock') ----------------------------

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How to block anonymous access and disallow user registration‏
by Jennifer Jackson 08 Aug '12

08 Aug '12

Re-Post to galaxy-dev On 8/6/12 11:59 AM, Joel Rosenberg wrote: > Hello, > > I've just set up my own instance of Galaxy running in AWS and had a > security question that I couldn't find an answer to on the wiki. > > I'd like to prevent people from hitting my public Amazon IP and using > Galaxy. Is t! here a way to prevent anonymous users from accessing any > part of Galaxy except a login prompt and have user registration be > invite-only (or perhaps turn it off completely once a handful of > accounts have been created)? > > Thanks, > > -Joel > > > ___________________________________________________________ > 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/ > -- Jennifer Jackson http://galaxyproject.org

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Workflows do not open anymore
by Björn Grüning 08 Aug '12

08 Aug '12

Hello, after commit 29680fa5c35e we are not able to open workflows anymore. The error message is: TypeError: <mako.template.Template object at 0x6dc8e10> is not JSON serializable And the problematic changeset is here: https://bitbucket.org/galaxy/galaxy-central/changeset/29680fa5c35e6c22a6b72… Hope that helps, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening(a)pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/

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