April 2015 - galaxy-dev - lists.galaxyproject.org

SSL/LDAP configuration for CloudMan/Galaxy
by David Kovalic 27 Apr '15

27 Apr '15

Hi, We are interested in running CloudMan/Galaxy with SSL and LDAP. After searching around on the internet it seems like this is achievable and probably not too difficult, but there is no current complete “cookbook recipe” for doing so, so I thought it best to ask questions before I go ahead and break stuff :) As I understand: · ngnix needs to have the LDAP module added, as the standard CM ngnix build doesn’t include this · ngnix needs to have a custom ngnix.conf file which specifies the use of SSL and LDAP · Galaxy need to have a custom configuration universe_wsgi.ini for LDAP use By searching online I can’t clearly figure out: · How to recompile (and persist across CM cluster termination/restart) a new version of ngnix · The best way to maintain and specify a custom ngnix.conf. Is it possible to do this by placing the custom ngnix.conf in the cluster S3 bucket and adding a configuration line specifying its URL (e.g. "nginx_conf_contents: https://s3.amazonaws.com/[cm bucket ID]/ngnix.conf") in persistent_data.yaml file in the CM S3 bucket? · Where do I make the modifications such that the changes to universe_wsgi.ini persist across CM cluster termination/restart? It would be great to get some experienced insight on how best to complete this configuration, and have it persist. Any guidance would be greatly appreciated. Thanks, David Kovalic

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planemo questions
by Christian Brenninkmeijer 27 Apr '15

27 Apr '15

Hi All, If there is a separate planemo mailing list please point me there. I have been planing with planemo and find it a great tools. This gives me two questions. 1. Why does planemo lint say: "CHECK: Help contains valid reStructuredText." But not throw an error when there is NO such information 2. Is there a way to do a test when there are multiple output files. For example a tool ways writes to two different files. Thanks in advance Christian

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splitting bams bai
by Roberto Alonso CIPF 27 Apr '15

27 Apr '15

Hello, I am writing some code in Galaxy for splitting bams. Up to know, I am following the ideas that Marco Albuquerque proposed in this thread http://dev.list.galaxyproject.org/Parallelism-using-metadata-td4666763.html . He proposed three ways of splitting: 1) by_rname -> splits the bam into files based on the chromosome 2) by_interval -> splits the bam into files based on a defined bp length, and does so across the entire genome present in the BAM file 3) by_read -> splits the bam into files based on the number of reads encountered (if multiple files, all other files match the interval as the first) As I think the easiest is the first one, I started with this option. First of all , I had to change line 82 of lib/galaxy/jobs/splitters/multi.py as that "if" didn't let the code to continue (I talked this in another thread). Next, I had to do some changes in lib/galaxy/datatypes/binary.py. I added a method "split" that creates the json for the script extract_dataset_parts.sh. Here, in the next code you can see that I call samtools -H in order to get the chromosome names, now I realized that I can get that information directly from metadatas in the input_datasets variable, so in the future I will change this. def split(cls, input_datasets, subdir_generator_function, split_params): # 1) by_rname -> splits the bam into files based on the chromosome # 2) by_interval -> splits the bam into files based on a defined bp length, and does so across the entire genome present in the BAM file # 3) by_read -> splits the bam into files based on the number of reads encountered (if multiple files, all other files match the interval as the first) if split_params is None: return if len(input_datasets) > 1: raise Exception("BAM file splitting does not support multiple files") input_file = input_datasets[0].file_name if 'split_mode' not in split_params: raise Exception('Tool does not define a split mode') elif split_params['split_mode'] == 'by_rname': log.debug("Attemping to split BAM file %s by chromosome", input_file) #First get bam header params = ["samtools", "view", "-H", input_file] output = subprocess.Popen( params, stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[0] output = output.split("\n") chrList = [] #Get chromosome list from the header. for line in output: fields = line.strip().split("\t") if fields[0].startswith("@SQ") and fields[1].startswith("SN:"): chrList.append(fields[1].split("SN:")[1]) # Write json for extract_dataset_parts for chrName in chrList: try: part_dir = subdir_generator_function() base_name = os.path.basename(input_file) part_path = os.path.join(part_dir, base_name) split_data = dict(class_name='%s.%s' % (cls.__module__, cls.__name__), output_name=part_path, input_name=input_file, args=dict(chromosome=chrName)) f = open(os.path.join(part_dir, 'split_info_%s.json' % base_name), 'w') json.dump(split_data, f) f.close() except Exception, e: log.error("Error: " + str(e)) raise else: raise Exception('Unsupported split mode %s' % split_params['split_mode']) split = classmethod(split) Well, this works correctly and writes the json as expected. Now I have to write the code that is called by scripts/extract_dataset_part.py (inside of extract_dataset_parts.sh) "cls.*process_split_file*(data)". So I created the next two function in the Bam class: def *process_split_file*(data): """ This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine) to create the input files for the Task. The parameters: data - a dict containing the contents of the split file """ args = data['args'] input_name = data['input_name'] output_name = data['output_name'] chromosome = args['chromosome'] commands = Bam.get_split_commands_chromosome(input_name, output_name, chromosome) for cmd in commands: if 0 != os.system(cmd): raise Exception("Executing '%s' failed" % cmd) return True process_split_file = staticmethod(process_split_file) def get_split_commands_chromosome(input_name, output_name, chromosome): params = ["samtools view -h " + input_name + " " + output_name + " " + chromosome] return params get_split_commands_chromosome = staticmethod(get_split_commands_chromosome) Which is my problem? That I need the .bai related with that dataset "input_name", I think is in a metadata table, but I don't know how to get it, Could you please help me with this? In any case, if you find that I am doing something wrong, or you have a better idea of implementing this, please don't hesitate to contact me. Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

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GCC2015 Registration is Open!
by Dave Clements 27 Apr '15

27 Apr '15

Hello all, We are tremendously pleased (and more than a little relieved) to announce that *registration for GCC2015 is now open <http://gcc2015.tsl.ac.uk/registration/>*. The 2015 Galaxy Community Conference <http://gcc2015.tsl.ac.uk/> includes 2 days of hackathons, 2 days of training, and a two day meeting <http://gcc2015.tsl.ac.uk/programme/> featuring accepted presentations, keynotes, poster sessions, lightning talks, birds-of-a-feather meetups, and plenty of networking. GCC2015 is hosted by The Sainsbury Laboratory <http://www.tsl.ac.uk/>, in Norwich, UK, and events run 4-8 July. Registration costs <http://gcc2015.tsl.ac.uk/registration/> depend on which events you register for <http://gcc2015.tsl.ac.uk/programme/>, your career stage/affiliation <http://gcc2015.tsl.ac.uk/registration/>, and when you register <http://gcc2015.tsl.ac.uk/registration/>*(register by 22 May - really, it will save you plenty).* Early bird registration starts at less than £40 / day for students and postdocs, and at £55 / day for other attendees from non-profits. You can also sign up for conference housing <http://gcc2015.tsl.ac.uk/logistics/#Lodging> during (and only during) registration. We apologize profusely for the delay in opening registration, and we thank you for your patience and faith. We promise the conference will againbe spectacular <https://wiki.galaxyproject.org/GalaxyProject/Statistics#Events> . Dave Clements <https://wiki.galaxyproject.org/DaveClements> and Martin Page <http://www.tsl.ac.uk/staff/martin-page/>, on behalf of the GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers/>. PS: *And don't forget the poster abstract <http://gcc2015.tsl.ac.uk/Abstracts> submission deadline is 1 May.* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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error in Galaxy (lefse)
by Borruso Luigimaria 26 Apr '15

26 Apr '15

Dear Galaxy-project staff, in the last two weeks, I have tried several time to use Lefse but it seems to have some problem. I always get the following message: Internal Server Error Galaxy was unable to successfully complete your request. An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. Thanks a lot Luigi Borruso, PhD Environmental Microbiology Faculty of Science & Technology Building K, Office 1.05 Free University of Bozen/Bolzano Piazza Università 5 I-39100 Bozen/Bolzano Italy Tel. +39 0471 017610 E-mail: luigimaria.borruso(a)unibz.it<mailto:lorenzo.brusetti@unibz.it> Website: www.unibz.it/sciencetechnology<http://www.unibz.it/sciencetechnology>

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Announcement: Galaxy Docker Image 15.03
by Björn Grüning 25 Apr '15

25 Apr '15

Hi all! We are proud to present you the next release of Galaxy Docker. https://github.com/bgruening/docker-galaxy-stable https://registry.hub.docker.com/u/bgruening/galaxy-stable/ A few highlights: * based on Galaxy 15.03, with all it's new awesome features * Docker image is now based on Ubuntu 14.04 * move all required Galaxy dependencies to toolshed/requirements * use Ansible roles to build large parts of the image * export the supervisord web-interface (port 9002) * enable Galaxy reports webapp on GALAXY_URL/reports * enable/disable services like FTP or Galaxy reports during start-up The IPython integration was also updated and has a few new libraries to make it more convenient for R users. A big thanks to John Chilton for his enormous support and constant input. The following new releases are available: * docker pull bgruening/galaxy-stable:latest_2015.01.13 * docker pull bgruening/galaxy-stable:15.03 * docker pull bgruening/galaxy-stable (-> currently 15.03) As usual feedback is more than welcome! Cheers, Bjoern

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InvalidRequestError: kombu.transport.sqlalchemy.Queue
by Asma Riyaz 25 Apr '15

25 Apr '15

Hi, I am receiving this traceback when I do restart Apache and not sure what to make of it: Exception in thread WorkflowRequestMonitor.monitor_thread: Traceback (most recent call last): File "/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/threading.py", line 530, in __bootstrap_inner self.run() File "/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/threading.py", line 483, in run self.__target(*self.__args, **self.__kwargs) File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 158, in __monitor self.__schedule( workflow_scheduler_id, workflow_scheduler ) File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 162, in __schedule invocation_ids = self.__active_invocation_ids( workflow_scheduler_id ) File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 191, in __active_invocation_ids handler=handler, File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/model/__init__.py", line 3254, in poll_active_workflow_ids WorkflowInvocation File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/session.py", line 1165, in query return self._query_cls(entities, self, **kwargs) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 108, in __init__ self._set_entities(entities) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 118, in _set_entities self._set_entity_selectables(self._entities) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 151, in _set_entity_selectables ent.setup_entity(*d[entity]) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 3036, in setup_entity self._with_polymorphic = ext_info.with_polymorphic_mappers File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/util/langhelpers.py", line 725, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 1877, in _with_polymorphic_mappers configure_mappers() File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 2589, in configure_mappers mapper._post_configure_properties() File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 1694, in _post_configure_properties prop.init() File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/interfaces.py", line 144, in init self.do_init() File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py", line 1549, in do_init self._process_dependent_arguments() File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py", line 1605, in _process_dependent_arguments self.target = self.mapper.mapped_table File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/util/langhelpers.py", line 725, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py", line 1522, in mapper argument = self.argument() File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/ext/declarative/clsregistry.py", line 283, in __call__ (self.prop.parent, self.arg, n.args[0], self.cls) InvalidRequestError: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined. This happens sometimes but when I shut down galaxy and re-start I don't get it anymore. Can someone guide me to a more permanent solution to this? Asma

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README.rst missing on Tool Shed display?
by Peter Cock 24 Apr '15

24 Apr '15

Hi all, I don't see tool README files on the main view of a repository any more. Is this a recent regression? e.g. https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools and https://testtoolshed.g2.bx.psu.edu/view/bgruening/deeptools should show the readme.rst file e.g. https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus and https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus should show the README.rst file This might be specific to restructured-text markup - I'd have to trawl the ToolShed looking for a plain text README file to check that. Regards, Peter

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History panel error
by Jose Juan Almagro Armenteros 24 Apr '15

24 Apr '15

Hello all, I have updated my Galaxy distribution today to the latest version 15.03 and the history panel is not being shown. The history seems to be there but Galaxy can't display the datasets. Even if I create a new history and I run a tool the dataset is not shown. It is just displayed an error which says: "An error occurred while getting updates from the server..." and the details shows this: { "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120 Safari/537.36", "url": "http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9…", "data": "", "options": { "data": {}, "silent": true, "parse": true, "emulateHTTP": false, "emulateJSON": false }, "xhr": { "readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}", "responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error", "responseHeaders": { "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r", "cache-control": "max-age=0,no-cache,no-store\r", "Transfer-Encoding": "chunked\r", "Server": "PasteWSGIServer/0.5 Python/2.7.3\r", "Connection": "close\r", "x-frame-options": "SAMEORIGIN\r", "content-type": "application/json\r" } }, "source": [], "user": { "username": "jose", "quota_percent": 0, "total_disk_usage": 101352147, "nice_total_disk_usage": "96.7 MB", "email": "jjalmagro(a)gmail.com", "is_admin": true, "tags_used": [], "model_class": "User", "id": "72ad249754f05d26" } } Do you have any idea what could go wrong? Thank you and best regards, Jose

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question about splitting bams
by Roberto Alonso CIPF 24 Apr '15

24 Apr '15

Hello, I ma trying ti write some code in order to give the possibility of parallelize some tasks. Now, I was with the problem of splitting a bam in some parts, for this I create this simple tool <parallelism method="multi" split_size="3" split_mode="number_of_parts" merge_outputs="output" split_inputs="input" ></parallelism> <command> java -jar /home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/chr_19_hg19_ucsc.fa -I $input -o $output 2> /dev/null; </command> <inputs> <param format="bam" name="input" type="data" label="bam"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs> But I have one problem, when I execute the tool it goes through this part of code (I am working in dev branch): *$galaxy/lib/galaxy/jobs/splitters/multi.py, line 75:* for input in parent_job.input_datasets: if input.name in split_inputs: this_input_files = job_wrapper.get_input_dataset_fnames(input.dataset) if len(this_input_files) > 1: log_error = "The input '%s' is composed of multiple files - splitting is not allowed" % str(input.name) log.error(log_error) raise Exception(log_error) input_datasets.append(input.dataset) So, it is raising the exception because this_input_files=2, concretely: ['/home/ralonso/galaxy/database/files/000/dataset_171.dat', '/home/ralonso/galaxy/database/files/_metadata_files/000/metadata_13.dat'], I guess that: *dataset_171.dat*: It is the bam file. *metadata_13.dat*: It is the bai file. So, Galaxy can't move on and I don't know which would be the best solution. Maybe change the *if* to check only non-metadata files? I think I should use both files in order to create the bam sub-files, but this would be inside the Bam class, under *binary.py* file. Could you please guide me before I mess things up? Thanks so much -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

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Shared Data Library issues with permissions
by Ganote, Carrie L 24 Apr '15

24 Apr '15

Hi Devs, Maybe I'm missing something, but I'm having trouble getting permissions right on the Data Libraries. I can reproduce this: As an admin, I go to Manage data libraries. On top right, I click Create new data library. Let's call it test. I Add a folder in test, called "more testing". I check the permissions of the library in Library Actions->Edit permissions and make sure that all roles associated are blank. I check permissions in more testing to make sure they are all blank. I click on Shared Data -> Data Libraries to see if I can view the files with the user perspective. I click on the Test library I just created: Data Library “Test” The data library 'Test' does not contain any datasets that you can access. I have a fairly recent (April 2015) update to Galaxy. Any advice? I first started having trouble getting access for a user to their own library; when I associated their role with their own folder, they still couldn't see anything they could access. I should at least get an empty folder. Sincerely, Carrie Ganote

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Serving a galaxy instance over Apache
by Asma Riyaz 24 Apr '15

24 Apr '15

Hi, I have been through previous issues regarding this issue. So far, I have included the rewrite Engine logic written in /etc/apache2/sites-available/defaults - looks like so: <VirtualHost *:80> ..... ..... RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /seq/SOFTWARE/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /seq/SOFTWARE/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /seq/SOFTWARE/galaxy/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /seq/SOFTWARE/galaxy/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /seq/SOFTWARE/galaxy/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://[my IP address]/$1 [P] I restarted apache after this and accessed : http://[my IP address]/galaxy but no webpage is found. Any advice on how I can proceed to configure the apache correctly? Thank you, Asma

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Re: [galaxy-dev] Galaxy on HPC and Bright Cluster Manager?
by David Trudgian 23 Apr '15

23 Apr '15

Hi Carlos, sorry for the slow reply. With a small 10 user setup (I assume just one group) your installation is probably going to be a lot less complex than ours. We are running services for users from multiple labs and departments, so a chief concern was making sure private datasets always stay private - which is relatively involved when using Galaxy to run jobs on a general-purpose shared cluster. I think if I had to recommend picking a job scheduler I would suggest SLURM since it's probably the most 'fashionable' choice at present. You also have the advantage that SLURM is used with Galaxy in the Galaxy docker image etc. which ensures people notice if the Galaxy->DRMAA->SLURM setup isn't working. I've also used Galaxy with GridEngine in the past, and that was fine - but is becoming a less common choice as a scheduler. Having said that, I don't think that the job scheduler needs to be your biggest concern. I would focus most on the file system and user account setup you are going to need. * How are you going to migrate from standalone Galaxy to a situation where your new cluster can see the Galaxy data files, tools etc. Are you purchasing storage with the cluster? If so do you move Galaxy onto that storage, or can you mount existing Galaxy data onto the cluster nodes? If you can do that, is your networking such that performance is sufficient for the type of analysis you are going to run? * Do you need to, or will you need to, keep track of per-user usage of the cluster for things that Galaxy will be running? If not then you can just have a galaxy user on your cluster and things are pretty easy for file permissions etc. If you need to track jobs per-user then it becomes more complex, and the solution depends on how much privacy you need for datasets, how your cluster will authenticate users etc. The filesystem and user accounts issues are, in my mind, the ones to focus on. You can always modify Galaxy's config to switch to a different job scheduler fairly easily. You cannot as easily move around large amounts of data, and reconcile local vs cluster user accounts, should that be necessary. Cheers, Dave Trudgian -----Original Message----- From: Carlos Lijeron [mailto:clijeron@hunter.cuny.edu] Sent: Wednesday, April 22, 2015 10:54 AM To: David Trudgian; John Chilton Cc: RODRIGO GONZALEZ SERRANO Subject: Re: [galaxy-dev] Galaxy on HPC and Bright Cluster Manager? Hello David, Thank you for the great feedback. We are at Hunter College in NYC, part of the City University of New York. We recently ordered the cluster which comes with Bright Cluster Management, and our PI wants to implement Galaxy for all the users (about 10) on the cluster and manage all job submissions through a job scheduler. So, to answer your question, we are not really using any scheduler at this point, but only a stand alone server with a local installation of Galaxy. Our Cluster should be assembled and installed by the end of May, so I¹m trying to gather as much information as possible in preparation for the deployment. Based on your experience, what do you think I should focus on to ensure we maximize outcome and reduce the possibility of mistakes? In other words, any lessons learned that you would like to share will be greatly appreciated. Thanks again, Carlos Lijeron. On 4/22/15, 10:34 AM, "David Trudgian" <David.Trudgian(a)UTSouthwestern.edu> wrote: >Carlo, > >We have Bright Cluster Manager in use on our cluster for node >provisioning etc. but the actual job scheduler in use in our case is >SLURM, which we use directly. > >Are you using one of the integrated workload managers such as SLURM / >SGE / TORQUE directly, or indirectly via cmsub? > >I guess the easiest way to come up with some kind of advice is if you >can provide an example of generic job script you are using on your system. >If you're using cmsub is it specifying a --wlmanager etc. > >DT > >-----Original Message----- >From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On >Behalf Of John Chilton >Sent: Wednesday, April 22, 2015 8:26 AM >To: Carlos Lijeron >Cc: galaxy-dev(a)lists.galaxyproject.org >Subject: Re: [galaxy-dev] Galaxy on HPC and Bright Cluster Manager? > >Hello Carlos, > > I have never heard of anyone running Galaxy with Bright Cluster >Manager (though hopefully someone will chime in if they have). If you >are interested in adding support it should be possible. One >complication is that Bright Cluster Manager doesn't appear to have a >DRMAA interface >(http://www.drmaa.org/) which is the most direct way to utilize new DRMs. >Without that my approach would be to build a new CLI runner: > >There are a few examples here that one can use as template: > >https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/jobs/runner >s/u >til/cli/job > >I guess you would have to write a new one targeting cmsub I guess - you >also need to be able to parse a job status somehow - I haven't figured >out how to do that from the documentation - but I assume there is a way. > >I looks like Bright supports running SGE, SLURM, and Torque on the >cluster - doing this and interfacing with one of those more common >options directly might be a better approach for Galaxy (and other users >if your cluster has them). > >-John > > > > > > > >On Wed, Apr 22, 2015 at 8:56 AM, Carlos Lijeron ><clijeron(a)hunter.cuny.edu> wrote: >> Good day everyone, >> >> >> >> Has anyone of you been able to implement Galaxy on a HPC using Bright >> Cluster Manager as the main DRM? I noticed that only a few have been >> known to work with Galaxy, but the list does not include Bright. Any >> advice/ideas will be greatly appreciated. >> >> >> >> TORQUE Resource Manager >> >> PBS Professional >> >> Open Grid Engine >> >> Univa Grid Engine (previously known as Sun Grid Engine and Oracle >> Grid >> Engine) >> >> Platform LSF >> >> HTCondor >> >> Slurm >> >> Galaxy Pulsar (formerly LWR) >> >> >> >> >> >> Thanks. >> >> >> >> >> >> Carlo >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this and other >> Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >___________________________________________________________ >Please keep all replies on the list by using "reply all" >in your mail client. To manage your subscriptions to this and other >Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > >To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > >________________________________ > >UT Southwestern > > >Medical Center > > > >The future of medicine, today. >

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Writing Auth Layer as WSGI Middleware
by Stephen Rosen 23 Apr '15

23 Apr '15

Hi All, I have a need for authentication as a layer in front of Galaxy which is more specialized than the available options -- specifically 3-legged OAuth against site of my choice. After looking into writing this in PHP and having the webserver (nginx) set remote_user, I decided to nix that approach for a couple of reasons -- one of which is that I don't have PHP experience. After a few discussions with other devs, I've decided that there are two easy options available to me: - Write a WSGI app which does authentication, and *proxies* authenticated requests to Galaxy with remote_user set. Since that's a WSGI app doing proxying, obvious code smell there - Write a WSGI middleware that wraps the existing Galaxy WSGI app, and passes authenticated requests directly to the Galaxy app That second solution seems much better, but I'm now faced with the question of "How do I do it?" Looking over the sample config, I see these lines: # The factory for the WSGI application. This should not be changed. paste.app_factory = galaxy.web.buildapp:app_factory I'm thinking that I could change that to my middleware, which will turn to `galaxy.web.buildapp` when the time comes. One problem I'm seeing is that my middleware and galaxy both have to run in the same virtualenv, so there's potential for dependency conflicts. The lib I want to use for this does rely on PyYAML and a few other things which Galaxy also needs, so that possibility is very real. Other than that hurdle, are there any gotchas I should be aware of with this approach? Are there similarly simple alternatives to this which I am not seeing? Ultimately, if I have to write an app that does proxying, I'd prefer that to the wide variety of highly effortful solutions I have envisioned. Those include, but are not limited to, a PAM which does the OAuth and doing Basic Authentication against that, just to give a flavor. Thanks very much for your help, -Stephen

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Galaxy Tool Shed security vulnerability
by Nate Coraor 23 Apr '15

23 Apr '15

*Please note: This notice affects Galaxy Tool Shed servers only. Galaxy servers are unaffected.* A security vulnerability was recently discovered by Daniel Blankenberg of the Galaxy Team that would allow a malicious person to execute arbitrary code on a Galaxy Tool Shed server. The vulnerability is due to reuse of tool loading code from Galaxy, which executes "code files" defined by Galaxy tool config files. Because the Tool Shed allows any user to create and "load" tools, any user could cause arbitrary code to be executed by the Tool Shed server. In Galaxy, administrators control which tools are loaded, which is why this vulnerability does not affect Galaxy itself. Although we recommend upgrading to the latest stable version (15.03.2), a fix for this issue has been committed to Galaxy versions from 14.08 and newer. If you are using Mercurial, you can update with (where YY.MM corresponds to the Galaxy release you are currently running): % hg pull % hg update release_YY.MM If you are using git, you can update with (assuming your remote upstream is set to https://github.com/galaxyproject/galaxy/) If you have not yet set up a remote tracking branch for the release you are using: % git fetch upstream % git checkout -b release_YY.MM upstream/release_YY.MM Otherwise: % git pull upstream release_YY.MM For the changes to take effect, *you must restart all Tool Shed server processes*. Credit for the arbitrary code execution fix also goes to my fellow Galaxy Team member Daniel Blankenberg. On behalf of the Galaxy Team, --nate

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Galaxy on HPC and Bright Cluster Manager?
by Carlos Lijeron 22 Apr '15

22 Apr '15

Good day everyone, Has anyone of you been able to implement Galaxy on a HPC using Bright Cluster Manager as the main DRM? I noticed that only a few have been known to work with Galaxy, but the list does not include Bright. Any advice/ideas will be greatly appreciated. TORQUE Resource Manager PBS Professional Open Grid Engine Univa Grid Engine (previously known as Sun Grid Engine and Oracle Grid Engine) Platform LSF HTCondor Slurm Galaxy Pulsar (formerly LWR) Thanks. Carlo

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Issue writing functional tool test with repeat tag in config
by Christy Shafer 22 Apr '15

22 Apr '15

Hello, I'm trying to format a test tag in a tool config for the public Tool Shed that includes a repeated input parameter. I followed the syntax suggested in the following archived galaxy-dev post (was unable to find much other guidance): http://git.net/galaxy-development-source-control/msg15241.html, but the config file must be invalid because my repository on the Tool Shed does not register as an installable Galaxy utility. Any guidance is much appreciated.. Below are the relevant config code sections: <inputs> <repeat name="Files" title="Join file"> <param name="joinMe" type="data" checked="yes" format="tabular" label="Join" /> <param name="joinCol" label="using column" type="data_column" data_ref="joinMe" /> </repeat> <param name="headerYes" type="select" label="Treat first line as header?"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> </inputs> <outputs> <data format="tabular" name="Joined_all" label="Multi-Join result"/> </outputs> <tests> <test> <param name="Files_0|joinMe" value="multi_join_serial_in1.tab" ftype="tabular"/> <param name="Files_0|joinCol" value="1"/> <param name="Files_1|joinMe" value="multi_join_serial_in2.tab" ftype="tabular"/> <param name="Files_1|joinCol" value="1"/> <param name="Files_2|joinMe" value="multi_join_serial_in3.tab" ftype="tabular"/> <param name="Files_2joinCol" value="2"/> <param name="headerYes" value="yes"/> <output name="Joined_all" value="multi_join_serial_out.tab" ftype="tabular"/> <test/> <tests/> Thanks for your help, CS

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Problem killing jobs (via Admin>Manage Jobs)
by Poole, Richard 21 Apr '15

21 Apr '15

Hi all, I am having an issue killing jobs via Admin>Manage Jobs. When I try to submit kills I see this in the Galaxy log: galaxy.jobs.runners.local WARNING 2015-04-19 15:55:03,089 stop_job(): 10374: no PID in database for job, unable to stop I have updated my local Galaxy server (via hg) and am currently running 17052:28113eee212. I am scared the issue is a database issue, however everything else and communication with the PostgreSQL database seems functional. Any help greatly appreciated :) Richard Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)

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GCC2015 Registration and Lodging Scholarship for US-Based Post-Docs and Students
by Dave Clements 21 Apr '15

21 Apr '15

Hello all, *We are pleased to offer registration <http://gcc2015.tsl.ac.uk/registration> and lodging <http://gcc2015.tsl.ac.uk/logistics/#Lodging> scholarships for GCC2015 for students and post-docs who are based in the United States, and who are members of historically underrepresented groups in life science research.* These scholarships cover registration costs <http://gcc2015.tsl.ac.uk/registration> for any GCC2015 events <http://gcc2015.tsl.ac.uk/proigramme> the recipients sign up for, and also covers lodging <http://gcc2015.tsl.ac.uk/logistics/#Lodging> during those events in the official conference lodging <http://gcc2015.tsl.ac.uk/logistics/#Lodging> on the nearby UEA campus. *The scholarships do not cover travel or other expenses.* To apply for a scholarship qualifying applicants need to 1. Submit a poster abstract <http://bit.ly/gcc2015sub>. *The deadline is May 1* 2. Have a faculty member / PI send a letter of recommendation to the Galaxy Community Fund Board <community-fund(a)lists.galaxyproject.org> no later than May 15. 3. Submit an application form <http://bit.ly/gcc2015scholarship>, no later than May 1. 4. Have sufficient funds to cover your travel and other expenses. Applicants will be notified of their scholarship status no later than May 19. Scholarships are funded by the *Galaxy Community Fund*. The Galaxy Community Fund was established with the surplus funds from GCC2014, and is currently administered by the GCC2014 organizers. Please do let us know if you have any questions, and we hope to see you at GCC2015 <http://gcc2015.tsl.ac.uk/>! Galaxy Community Fund Board <community-fund(a)lists.galaxyproject.org> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Adding a dataset to a dataset list breaks "Run this job again"
by Brian Claywell 21 Apr '15

21 Apr '15

While testing an upgrade from latest_2014.10.06 to GitHub release_15.03 branch (cloned today) I ran into an issue trying to use the "Run this job again" functionality on a dataset. I was playing with creating dataset lists using "Operations on multiple datasets" and noticed that after adding a dataset to a dataset list, trying to run the job again fails. This is the tool form that gets displayed: [image: Inline image 1] Additionally an error is logged: galaxy.tools ERROR 2015-04-15 21:58:53,258 'HistoryDatasetAssociation' object has no attribute 'collection' Deleting the dataset list makes no difference. However, if I copy this dataset to a new history and click "Run this job again", no error occurs and the proper tool form appears. If I then add the dataset in the new history to a dataset list, the error reappears. Cheers, Brian -- Brian Claywell | programmer/analyst Matsen Group | http://matsen.fredhutch.org <http://matsen.fhcrc.org/> Fred Hutchinson Cancer Research Center

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metadata in parallelization
by Roberto Alonso 21 Apr '15

21 Apr '15

Hello, I am writing some code to enable parallelization for some tool wrappers. First, I did it for simple bwa wrapper, but now I am modifying toolshed.g2.bx.psu.edu/repos/devteam/bwa/c71dd035971e/bwa/bwa-mem.xml to check if the code would work with this wrapper. So, I wrote some code that I thing was necessary in order to merge some bam and I added the parallelism tag (in bold) to the config file: <tool id="bwa_mem" name="BWA-MEM" version="0.1"> <macros> <import>bwa_macros.xml</import> </macros> <requirements> <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> <requirement type="package" version="1.1">samtools</requirement> </requirements> <description>- map medium and long reads (> 100 bp) against reference genome</description> *<parallelism method="multi" split_size="3" shared_inputs="ref_file" split_mode="number_of_parts" merge_outputs="bam_output" split_inputs="fastq_input1,fastq_input2" ></parallelism>* <command> ... So, everything works well, and the resulting bam from parallelization mode and without the parallelization mode is the same but the Galaxy log throws an error regarding metadata, it says something like this: galaxy.jobs.splitters.multi DEBUG 2015-04-17 09:54:58,335 merge finished: /home/ralonso/galaxy/database/files/000/dataset_198.dat galaxy.jobs.runners.tasks DEBUG 2015-04-17 09:54:58,473 executing external set_meta script for job 200: python /home/ralonso/galaxy/database/tmp/set_metadata_E5fGIE.py /home/ralonso/galaxy/database/tmp/tmpHS8Byo /home/ralonso/galaxy/database/job_working_directory/000/200/galaxy.json /home/ralonso/galaxy/database/tmp/metadata_in_HistoryDatasetAssociation_198_yOGiQG,/home/ralonso/galaxy/database/tmp/metadata_kwds_HistoryDatasetAssociation_198_nAsQoq,/home/ralonso/galaxy/database/tmp/metadata_out_HistoryDatasetAssociation_198_I_cLs4,/home/ralonso/galaxy/database/tmp/metadata_results_HistoryDatasetAssociation_198_qhjzoV,/home/ralonso/galaxy/database/files/000/dataset_198.dat,/home/ralonso/galaxy/database/tmp/metadata_override_HistoryDatasetAssociation_198_ScKLqH Traceback (most recent call last): File "/home/ralonso/galaxy/database/tmp/set_metadata_E5fGIE.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() ImportError: No module named galaxy_ext.metadata.set_metadata galaxy.jobs.runners.tasks DEBUG 2015-04-17 09:54:58,624 execution of external set_meta finished for job 200 *galaxy.datatypes.metadata DEBUG 2015-04-17 09:54:58,714 setting metadata externally failed for HistoryDatasetAssociation 198: External set_meta() not called* When using no parallelization mode, there is no problem, also because Galaxy doesn't go through this part of code, I mean it doesn't execute this. I see that Galaxy have to do something with metada attributes, but what is t trying to do? is there any way to solve this? Thank you very much Regards, Roberto

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pbs/torque config
by Beginner TI 21 Apr '15

21 Apr '15

Hi, I'm trying to enable the capability to submit jobs to a pbs cluster, however I am quite confused by the documentation. I don't know where I could specify the pbs server. I saw the following on the page: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster 1 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <plugins> 2 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/> 3 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> </plugins> 4 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <destinations default="pbs_default"> 5 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <destination id="pbs_default" runner="pbs"/> 6 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <destination id="other_cluster" runner="pbs"> 7 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <param id="destination">@other.cluster</param> 8 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> </destination> 9 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <destination id="long_jobs" runner="pbs"> 10 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param> 11 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> <param id="-p">128</param> 12 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> </destination> 13 <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb8b…> </destinations> is this <param id="destination"> the place you specify where your pbs/torque server? and the syntax is to prepend a '@' to the server name? for example, should a most basic config look like: <plugins> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"> </plugins> <destinations default="pbs"> <destination id="pbs" runner="pbs" > <param id="destination">@pbs_server_full_name</param> <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param> <param id="-q">myqueue</param> </destination> <destinations> I searched online and to my surprise I didn't find any useful information, or any working sample...please give me a hand guys! Thanks! Rui

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Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)
by Dooley, Damion 20 Apr '15

20 Apr '15

I was successful getting library dataset selection and form submission to happen within tool form tool form input <param type="library_data" ...> - Yay! But it appears one last fix (besides the "url: "/visualization/list_libraries",' bug) is needed to enable history tool item to be RERUN. So if a galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :<( ***************** For others who may need... tool form's param: <param name="library_datasets" type="library_data" label="Reference Bin file" help="Select one reference bin at a time from the popup window's Reference Bin library."/> <command> tag contents.... #if $library_datasets -B " #for $i, $dataset in enumerate($library_datasets) #$dataset.get_file_name() $dataset.id #end for " #end if Successfully submits either the full file path of selected dataset, or its id. ***************** However trying to rerun this history tool item gets us an error (not related to the above <command> contents): Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'int' object has no attribute 'id' .... Module galaxy.tools.parameters.basic:146 in value_to_basic view >> return self.to_string( value, app ) Module galaxy.tools.parameters.basic:2406 in to_string app <galaxy.app.UniverseApplication object at 0x59a0710> ldda 331 self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090> value [331] >> return [ldda.id for ldda in value] AttributeError: 'int' object has no attribute 'id' which is in /lib/galaxy/tools/parameters/basic.py: class LibraryDatasetToolParameter( ToolParameter ): """ Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. """ ... def to_string( self, value, app ): if not value: return value return [ldda.id for ldda in value] "Value" is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just "id" but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing "Reference Bin file" as a string label of an object?: Input Parameter Value Note for rerun BLAST results as XML 240: megablast Pasted Entry vs 16SMicrobial.fasta Reference Bin file [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>] Tabular Report Column Labels Short name HTML Report template templates.html_report ******************************** The other bug: 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy installs that have a prefix so that needs adjustment: $(".add-librarydataset").click(function() { var link = $(this); $.ajax({ url: "/visualization/list_libraries",

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April GalaxyAdmins Meetup: Video and Slides are now available
by Dave Clements 20 Apr '15

20 Apr '15

Hi all, Slides from both talks and video of the whole meetup are now available at https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16 Many thanks to Carrie and Sam for presenting. See you at the next meetup June 18! Dave C On Thu, Apr 16, 2015 at 7:34 AM, Dave Clements <clements(a)galaxyproject.org> wrote: > Hello all, > > GalaxyAdmins is starting in about 25 minutes. The room is here: > > https://connect.johnshopkins.edu/galaxyadmins201504/ > > It takes a few minutes to navigate through Flash, so connecting a few > minutes early is encouraged. > > Thanks, > > Dave C > > > > On Wed, Apr 15, 2015 at 9:14 AM, Dave Clements <clements(a)galaxyproject.org > > wrote: > >> Hello all, >> >> Just a reminder that the April GalaxyAdmins online meetup is tomorrow, >> Thursday, at 5pm Central European Summer Time. See >> https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16 >> for details. A link to the meetup will be posted about an hour before the >> meetup. >> >> Thanks, >> >> Dave C >> >> On Thu, Apr 9, 2015 at 12:58 PM, Dave Clements < >> clements(a)galaxyproject.org> wrote: >> >>> Hello all, >>> >>> The April 2015 GalaxyAdmins meetup >>> <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16> >>> will be held online on Thursday, 16 April (a week from today). We'll meet >>> at 5pm Central European Summer Time (see your local time >>> <http://bit.ly/1EFUf0M>). >>> >>> Carrie Ganote <http://www.researchgate.net/profile/Carrie_Ganote> from >>> the National Center for Genome Analysis Support (NCGAS) >>> <http://ncgas.org/> and Pervasive Technology Institute >>> <http://pti.iu.edu/> at Indiana University will talk about her Galaxy >>> work with Trinity, IU Galaxy, and the Open Science Grid. And Sam >>> Guerler <https://wiki.galaxyproject.org/guerler> of the Galaxy Team >>> will also discuss recent work to update Galaxy's tool forms. >>> >>> GalaxyAdmins <https://wiki.galaxyproject.org/Community/GalaxyAdmins> is >>> a discussion group for Galaxy community members who are responsible for >>> Galaxy installations. Please see the meetup page ( >>> http://bit.ly/gxyadm201504) for more details. >>> >>> Hope to see (hear?) you there, >>> >>> Dave C (channeling Hans-Rudolf Hotz) >>> >>> -- >>> http://galaxyproject.org/ >>> http://getgalaxy.org/ >>> http://usegalaxy.org/ >>> https://wiki.galaxyproject.org/ >>> >> >> >> >> -- >> http://galaxyproject.org/ >> http://getgalaxy.org/ >> http://usegalaxy.org/ >> https://wiki.galaxyproject.org/ >> > > > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GCC2015 Oral Presentation Abstract Submission closes 20 April
by Dave Clements 20 Apr '15

20 Apr '15

Hello all, Just a reminder that oral presentation abstract submission for GCC2015 closes on Monday, 20 April, 5 days from now. Poster submission closes 1 May. See http://gcc2015.tsl.ac.uk/Abstracts for more. The 2015 Galaxy Community Conference is an opportunity to share your work with 200+ other researchers working in data-intensive biology. GCC2015 features 2 days of (2 different) hackathons, 2 days of training, and 2 days of meeting, posters, presentations, birds of a feather, and networking. See http://gcc2015.tsl.ac.uk/ for more on GCC2015. Looking forward to seeing you in July in Norwich! Dave C. On Wed, Feb 25, 2015 at 12:04 AM, Dave Clements <clements(a)galaxyproject.org> wrote: > Hello all, > > *We are pleased to announce that abstract submission for Oral and Poster > Presentations <http://gcc2015.tsl.ac.uk/Abstracts> at the 2015 Galaxy > Community Conference (GCC2015) <http://gcc2015.tsl.ac.uk/> is now open.* > > Abstract submission <http://gcc2015.tsl.ac.uk/Abstracts> for oral > presentations closes 10 April, and poster submission closes 1 May. Poster > authors will be notified of acceptance status within two weeks of > submission, while oral presentation authors will be notified no later than > 24 April. *Please consider presenting your work. If you are dealing with > big biological data, then this meeting wants to hear about it.* > > *About GCC2015* > > GCC2015 <http://gcc2015.tsl.ac.uk/> is hosted by The Sainsbury Lab > <http://www.tsl.ac.uk/>, in Norwich, United Kingdom > <http://www.visitnorwich.co.uk/>, in July 2015. GCC has been expanded > this year and will now offer two hackathons, two Training Days, and a two > day conference <http://gcc2015.tsl.ac.uk/programme/>. The Training Days > <http://gcc2015.tsl.ac.uk/training-day/> cover 15 different topics > spanning the full Galactic spectrum of topics. *Take a look > <http://gcc2015.tsl.ac.uk/programme/>.* > > Thanks, > > GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers/> > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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