- galaxy-user - lists.galaxyproject.org

Directly extracting results from Galaxy
by Jeff Shrager 05 Oct '09

05 Oct '09

We (BioBike) would like to do to Galaxy what Galaxy does to the UCSC browser, that is, be able to UI+programmatically (i.e., without download/upload of tables) get data from Galaxy to BioBike so that a BioBike user can then carry out next-level-up symbolic analysis on the data that has been molded, folded, and joined by Galaxy. Can someone point me to a description of the API that would enable us to do this? Thanks!

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varying number of output files in XML
by Matthias Dodt 05 Oct '09

05 Oct '09

Hi galaxy-users! I wrote a tool that splits a FASTA file into n output files, each one of a predefined maximum size. The program could return the number of files or a list of filenames... Is it possible to define the number of outputs dynamically (nr of output files dependent on input-filesize)? Thanks! till now i experimented with: <tool id="seqan_splitter_1" name="FASTA splitter"> <description>Splits input files into pieces of desired size</description> <command interpreter="python"> ./tools/RNA-seq/fasta-splitter/fasta-splitter.py --maxsize $size 2> $log_report </command> <inputs> <param name="source" type="data" format="fasta" label="input fasta file"/> <param name="size" type="integer" label="Size in Megabyte of each output file" value="500" optional="false"/> <param name="files" type="hidden" value="10"/> </inputs> <outputs> #for $i < $files <data format="fasta" name="\$i" label="Splitted file"/> #end for <data format="text" name="log_report" label="Detailed log report from splitter"/> </outputs> </tool>

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Sharing histories use case (another rant)
by Assaf Gordon 03 Oct '09

03 Oct '09

Another small usability issue... Use case: I want to share an existing history by link. 1. click on "options" button 2. click on "Stored By you" link (not very intuitive - one needs to read the grayed line ABOVE the link for the complete sentence: "List Your Histories Stored By You" ... usually it is recommended that the link itself contains the verb, like "List Your Histories" ). 3. Scroll to the page containing the desired history, no way to find it if I didn't tag it. 4. find the history, click on the little triangle next to it. 5. from the popup menu, select "share" 6. see the share page, realize this is sharing only by email, not by link - oops. 7. go back to history list. 8. again scroll to the right page. 9. Select the check-box next to the history 10. click on "Enable Import Via Link" 11. You are "jumped" back to page one. (arrgg!!! pages!!!!) 12. scroll again to the right page. 13. see the "importable" link next to the desired history. click it. 14. you get a page of ALL your shared histories, not sorted by any understandable way (time of sharing?) 15. manually search for the right history (by name). 16. copy link. 17. profit! I love galaxy, but sometimes it drives me crazy ;) -gordon.

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"Pages" in history list (short rant)
by Assaf Gordon 03 Oct '09

03 Oct '09

(My galaxy's not working, I have lots of time to write emails...) There's a new "pages" feature on the main galaxy site (was it introduced just yesterday?). It almost gave me a heart attack... There's no clear indication of division to pages (like a big shiny "next" button) and the links to the 1/2/3/4 pages are really tiny. For a second I thought all my old histories were gone. That being said, I really don't like this feature. On my internal galaxy (which is not upgraded yet) I have more than 250 histories. That's 25 pages (!). The histories are not tagged (since tagging is a new feature) - so there's no way of filtering them. Without pagination, all my histories are shown on one page, and I can use my browser's "find" function to look for a history by name (or just sort by date and scroll down the list). Why do I need division to pages ? Please note that almost all web sites that do use pages, offer a global "search" button (not just tag search) - so in practice (if the search engine is good) - there's no need to go to the "next" page. This is not the case in Galaxy. Think about how much work I have to do in order to find a history, If I didn't tag it (or if I forgot the tag name) - way too taxing. Also, the links themselves are very very small - it might make me sound like a grumpy bitter old man (which I am), but navigating galaxy with all those small triangle drop-down menus and small links becomes an exercise in hand-eye coordination and fine motor skills. Not all galaxy users are computer-savvy, they don't all swoosh and pinch and swap (or whatever you mac people do with the mouse). Please keep galaxy easy and accessible. Just my two cents, - gordon.

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How to get a list of coding exons in which each exon is represented once.
by Rehman, Atteeq (NIH/NIDCD) [F] 01 Oct '09

01 Oct '09

Hey everyone, I am a new galaxy user. I am trying to upload coding exons of specific region from ucsc genome browser but I end up with loading coding exons of all splice variants/isoforms. As a result some exons are repeated many times (depending upon how many isoforms the crossponding gene has) which I don't want. Can somebody help me how can I have a list of coding exons in which each exon is represented only once irrespective of how many splice variants/isoforms the gene has? Thanks a lot [cid:image001.jpg@01CA41C8.B3A28E40] Atteeq Ur Rehman Visiting Fellow National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Room 2A-19, 5 Research court, Rockville, MD, USA, 20850. Lab Ph. No. 301-402-9059

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Shortening sequences?
by Thomas Haverkamp 01 Oct '09

01 Oct '09

Hi All, I have a little how to do question and was hoping somebody knows the answer? I have a metagenomic data set with reads of lengths between 100 and 1000 bp. Now I want to create a dataset from my original dataset, with sequences of exact 200bp. I know I can use the filter tool to extract all reads longer than 199bp from the original data set. But then I want to cut off all the sequence bit that is longer than 200bp. so I end up with only a dataset of exactly 200bp. Does anybody know how I can do that in Galaxy. I was thinking of some of the EMBOSS tools, but they only see the first sequence and not all the other sequences in my Fasta file? Any ideas are welcome. Cheers Thomas Dr. Thomas H.A. Haverkamp Centre for Ecological and Evolutionary Synthesis (CEES) Dept. of Biology University of Oslo P.O. Box 1066 Blindern 0316 Oslo Norway Phone: +47 22 85 44 00 Mobile: +47 48 09 49 32 E-mail: thhaverk(a)bio.uio.no Skype: Thomieh73

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Composing Workflows
by Philippe Veber 29 Sep '09

29 Sep '09

Is it possible to compose workflows that is, see workflows as functions just like basic functionalities are ? Philippe.

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Integration of different datasources
by Matthias Dodt 28 Sep '09

28 Sep '09

Hi galaxy users! We would like to integrate a new datasource in our galaxy system. We want data to be inserted into galaxy via copying them directly from fileservers instead of uploading them through a http connection- maybe via some browser-based "explorer" who gives access to certain folders- Is there any galaxy-build in feature which may support something like this? thanks! greetings

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after copy of galaxy not starting
by Andreas Kuntzagk 24 Sep '09

24 Sep '09

Hi, to run a second copy of local galaxy I just copied the whole directory (cp -ra <old_dir> <new_dir>) I then just edited the universe_wsgi.ini to use a different port. Now when I start run.sh in <new_dir> I get following error: galaxy.jobs INFO 2009-09-24 13:03:27,136 job stopper started Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> command.run() File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 78, in run File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 117, in invoke File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 212, in run File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 227, in command File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 250, in loadapp File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 214, in loadobj File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 606, in create File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 99, in invoke File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "<old_dir>/lib/galaxy/web/buildapp.py", line 68, in app_factory File "<old_dir>/lib/galaxy/web/buildapp.py", line 38, in add_controllers File "<new_dir>/lib/galaxy/web/controllers/page.py", line 9, in <module> class PageListGrid( grids.Grid ): NameError: name 'grids' is not defined As you may notice there are some files in the stacktrace from old_dir. Even more confusing is, that I renamed <old_dir> in the meantime. So these files are nonexistant. Where are these pathes hardcoded? regards, Andreas

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Bug: using the python builtin "id" as parameter or variable name
by Andreas Kuntzagk 21 Sep '09

21 Sep '09

Hi, we encountered this problem when trying to clone a shared workflow: ... File '/data/bioinformatics/galaxy/lib/galaxy/web/security/__init__.py', line 45 in decode_id return int( self.id_cipher.decrypt( id.decode( 'hex' ) ).lstrip( "!" ) ) AttributeError: 'builtin_function_or_method' object has no attribute 'decode' (full error message attached) So looks like the python builtin "id" is used in a few places - which causes problems. Don't know why nobody else encountered this. For reasons explained regarding the other bug I can't switch to a newer version then 2690 at the moment but from bitbucket it seems this is still there. regards, Andreas 141.80.188.104 - - [21/Sep/2009:16:44:47 +0200] "GET /history/list_shared HTTP/1.1" 200 - "http://141.80.186.51:8080/" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9" 141.80.188.104 - - [21/Sep/2009:16:45:01 +0200] "POST /history/list_shared?sort=-update_time HTTP/1.1" 500 - "http://141.80.186.51:8080/history/list_shared" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9" Error - <type 'exceptions.AttributeError'>: 'builtin_function_or_method' object has no attribute 'decode' URL: http://141.80.186.51:8080/history/list_shared?sort=-update_time File '/data/bioinformatics/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ File '/data/bioinformatics/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py', line 80 in __call__ File '/data/bioinformatics/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ File '/data/bioinformatics/galaxy/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/framework/__init__.py', line 69 in decorator return func( self, trans, *args, **kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/controllers/history.py', line 280 in list_shared return self.clone( trans, id, **new_kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/framework/__init__.py', line 69 in decorator return func( self, trans, *args, **kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/controllers/history.py', line 751 in clone history = get_history( trans, history_id, check_ownership=False ) File '/data/bioinformatics/galaxy/lib/galaxy/web/controllers/history.py', line 781 in get_history id = trans.security.decode_id( id ) File '/data/bioinformatics/galaxy/lib/galaxy/web/security/__init__.py', line 45 in decode_id return int( self.id_cipher.decrypt( id.decode( 'hex' ) ).lstrip( "!" ) ) AttributeError: 'builtin_function_or_method' object has no attribute 'decode' CGI Variables ------------- CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded' HTTP_ACCEPT: 'application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=eb142648ac45b770fb93d51daf5785c6dd869b6b4503e8d7958db670bf3f993b3c3866342008fd05' HTTP_HOST: '141.80.186.51:8080' HTTP_ORIGIN: 'http://141.80.186.51:8080' HTTP_REFERER: 'http://141.80.186.51:8080/history/list_shared' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9' PATH_INFO: '/history/list_shared' QUERY_STRING: 'sort=-update_time' REMOTE_ADDR: '141.80.188.104' REQUEST_METHOD: 'POST' SERVER_NAME: '141.80.186.51' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- __file__: '/data/bioinformatics/galaxy/universe_wsgi.ini' admin_users: 'dominic.tolle@mdc-berlin.de,matthias.dodt@mdc-berlin.de' brand: '"It\'s full of stars!"' bugs_email: 'mailto:dominic.tolle@mdc-berlin.de' database_file: 'database/universe.sqlite' datatype_converters_config_file: 'datatype_converters_conf.xml' datatype_converters_path: '/data/bioinformatics/galaxy/lib/galaxy/datatypes/converters' datatype_indexers_path: '/data/bioinformatics/galaxy/lib/galaxy/datatypes/indexers' debug: 'False' default_cluster_job_runner: 'sge:///' error_email_to: 'dominic.tolle(a)mdc-berlin.de' file_path: 'database/files' gbrowse_display_sites: 'main,test' here: '/data/bioinformatics/galaxy' id_secret: 'changethisinproductiontoo' job_queue_cleanup_interval: '30' job_scheduler_policy: 'galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin' log_events: 'True' log_level: 'DEBUG' log_memory_usage: 'False' mailing_join_addr: 'galaxy-user-join(a)bx.psu.edu' new_file_path: 'database/tmp' sendmail_path: '/usr/sbin/sendmail' session_data_dir: '/data/bioinformatics/galaxy/database/beaker_sessions' session_key: 'galaxysessions' session_secret: 'changethisinproduction' session_type: 'file' set_metadata_externally: 'False' start_job_runners: 'sge' static_cache_time: '360' static_dir: '/data/bioinformatics/galaxy/static/' static_enabled: 'True' static_favicon_dir: '/data/bioinformatics/galaxy/static/favicon.ico' static_images_dir: '/data/bioinformatics/galaxy/static/images' static_scripts_dir: '/data/bioinformatics/galaxy/static/scripts/' static_style_dir: '/data/bioinformatics/galaxy/static/june_2007_style/blue' tool_config_file: 'tool_conf.xml' tool_data_path: 'tool-data' tool_path: 'tools' ucsc_display_sites: 'main,test,archaea' use_beaker_session: 'True' use_interactive: 'False' use_lint: 'False' use_new_layout: 'true' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x2efafd0> paste.cookies: (<SimpleCookie: galaxysession='eb142648ac45b770fb93d51daf5785c6dd869b6b4503e8d7958db670bf3f993b3c3866342008fd05'>, 'galaxysession=eb142648ac45b770fb93d51daf5785c6dd869b6b4503e8d7958db670bf3f993b3c3866342008fd05') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x2e57d90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xcde250> paste.parsed_querystring: ([('sort', '-update_time')], 'sort=-update_time') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_post_vars: (MultiDict([('id', '15a3f866c4811e6a'), ('operation', 'Clone')]), <FakeCGIBody at 332de90 viewing MultiDict([('id...e')])>) webob._parsed_query_vars: (MultiDict([('sort', '-update_time')]), 'sort=-update_time') wsgi process: 'Multithreaded' ------------------------------------------------------------

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