March 2011 - galaxy-dev - lists.galaxyproject.org

Default value for data_column not working?
by Peter Cock 14 May '14

14 May '14

Hi all, I'm trying to write a new tool working with tabular data (specifically a Reciprocal Best Hits (RBH) tool using BLAST style tabular output). I want the user to be able to choose a column number (from one of the input files), but I have a default column in mind. However, Galaxy doesn't seem to obey the default column number: <inputs> <param name="a_vs_b" type="data" format="tabular" label="Hits from querying A against B" description="Tabular file, e.g. BLAST output" /> <param name="b_vs_a" type="data" format="tabular" label="Hits from querying B against A" description="Tabular file, e.g. BLAST output" /> <param name="id1" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="1" label="Column containing query ID" help="This is column 1 in standard BLAST tabular output" /> <param name="id2" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="2" label="Column containing match ID" help="This is column 2 in standard BLAST tabular output"/> <param name="score" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="12" label="Column containing containing score to rank on" help="The bitscore is column 12 in standard BLAST tabular output"/> </inputs> I've tried giving the default column value numerically (as shown), and also using value="c2" etc. Regardless, Galaxy just defaults to the first column. Is this a bug, or am I doing something wrong? Thanks, Peter

3 9

Re: [galaxy-dev] [galaxy-user] Inquiring
by Nate Coraor 04 Nov '13

04 Nov '13

Hi Yan, I've moved this discussion to the galaxy-dev list since it pertains to a local installation of Galaxy. Responses to your questions follow, in-line. Yan Luo wrote: > Dear Sir, > > (1)We installed Galaxy, but recently the user can't registered and got the > following error, how can we fix it? > > Sever error > An error occurred. See the error logs for more information.(To turn debug on > to display ...). Since debug = False in universe_wsgi.ini, you should be able to find a more detailed error message in the log file. If starting Galaxy with: % sh run.sh --daemon The default log file is 'paster.log' in Galaxy's root directory. > (2) Could you please let me know if there is any command to stop galaxy? If starting with the --daemon flag (as above), you can use: % sh run.sh --stop-daemon If running in the foreground, you can use Ctrl-C to terminate the process. There is a recent bug whereby Ctrl-C is ineffective on some platforms under Python 2.6 - in this case you will have to kill/pkill the process manually. We are working on a fix for the latter. > (3) If I reset universe_wsgi.ini file and want to set an administrator > user(I can add a line in the above file), how can I get the password? Should > I stop galaxy(See question 2) first? then run "./setup.sh" and "./run.sh". setup.sh would have only been necessary prior to running Galaxy the first time, however, this step has recently been removed. If you are referencing documentation that still refers to setup.sh, please let us know so we can update it - I did notice this was still on the "Production Server" page, so I removed it from there. You no longer need to run setup.sh at all. > (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be generated? > if I want to change this file,should I edit it before "run.sh" and after > "setup.sh". Is it right? setup.sh and its replacements in run.sh and the Galaxy application itself never overwrite files, they only create files from sample files if they do not exist. > (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and > "./setup.sh"(./run.sh), which one is correct under Linux? Both syntaxes are effectively the same in most cases. --nate > > Looking forward to hearing from you. > > Best Wises, > > Yan Luo, Ph.D. > NIH > <http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,> > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

4 7

Puzzling test failure with data_column parameter
by Peter Cock 24 Apr '13

24 Apr '13

Hi all, I'm working on a FASTA filter script, as per this email: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003819.html Current code here: http://bitbucket.org/peterjc/galaxy-central/src/c3ac6d7a02f7/ I've added a basic test, but it won't run (see output below). I think the interesting bit of the error output is this exception: cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control, coming from function set_form_control_value in the twill.utils module. This is something to do with the columns parameter, a multiselect option referencing the columns in this tabular file. Removing the validator makes no difference. However, if I change the columns parameter to a plain text parameter, the test passes: $ hg diff diff -r c3ac6d7a02f7 tools/fasta_tools/fasta_filter_by_id.xml --- a/tools/fasta_tools/fasta_filter_by_id.xml Tue Nov 23 11:37:35 2010 +0000 +++ b/tools/fasta_tools/fasta_filter_by_id.xml Tue Nov 23 14:03:31 2010 +0000 @@ -4,9 +4,7 @@ <inputs> <param name="input_fasta" type="data" format="fasta" label="FASTA file to filter on the identifiers"/> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTA identifiers"/> - <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> - <validator type="no_options" message="Pick at least one column"/> - </param> + <param name="columns" type="text" label="Column(s) containing FASTA identifiers" /> </inputs> <outputs> <data name="output_pos" format="fasta" label="With matched ID" /> I've tried searching the provided wrappers for similar examples (column multi-select from a tabular file). I found filters/uniq.xml (works but uses a bed file rather than a simple tabular file) and stats/cor.xml (needs R and rpy which I don't have installed yet) which have tests, and finally plotting/bar_chart.xml which has no unit tests. Would someone familiar with the internals of the Galaxy tests and how they set tool parameters be able to try reproducing this for me? The branch has all the unit test files required, and there are no new dependencies needed. Thank you, Peter -- Here is the output (on Linux - other tests tried pass): $ ./run_functional_tests.sh -id fasta_filter_by_id ... nose.plugins.manager DEBUG 2010-11-23 13:59:32,958 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2010-11-23 13:59:32,961 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTestDiff nose.plugins.manager DEBUG 2010-11-23 13:59:32,962 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML Filter sequences by ID ( fasta_filter_by_id ) > Test-1 ... galaxy.tools.actions.upload_common INFO 2010-11-23 13:59:34,905 tool upload1 created job id 1 galaxy.jobs DEBUG 2010-11-23 13:59:42,709 dispatching job 1 to local runner galaxy.jobs INFO 2010-11-23 13:59:42,899 job 1 dispatched galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:43,213 executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:44,033 execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs DEBUG 2010-11-23 13:59:44,414 job 1 ended galaxy.tools.actions.upload_common INFO 2010-11-23 13:59:49,927 tool upload1 created job id 2 galaxy.jobs DEBUG 2010-11-23 13:59:50,067 dispatching job 2 to local runner galaxy.jobs INFO 2010-11-23 13:59:50,702 job 2 dispatched galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:52,059 executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:52,874 execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs DEBUG 2010-11-23 13:59:53,420 job 2 ended base.twilltestcase DEBUG 2010-11-23 13:59:53,747 In submit_form, continuing, but caught exception: cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control base.twilltestcase DEBUG 2010-11-23 13:59:54,488 ## files diff on /home/pjcock/repositories/galaxy-central/test-data/four_human_proteins_filter_a.fasta and /tmp/tmpijWxYGfour_human_proteins_filter_a.fasta lines_diff=0, found diff = 61 FAIL ====================================================================== FAIL: Filter sequences by ID ( fasta_filter_by_id ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", line 160, in test_tool self.do_it( td ) File "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", line 101, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes ) File "/home/pjcock/repositories/galaxy-central/test/base/twilltestcase.py", line 656, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 1 different than expected, difference (using diff): --- local_file +++ history_data @@ -1,2 +1,61 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF +SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK +REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER +VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD +CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF +HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG +GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS +DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD +LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP +DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT +IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE +ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY +QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV +ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD +KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE +NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA +QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK +APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR +HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS +WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ +SQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL +QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL +VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE +ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG +CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC +TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL -------------------- >> begin captured stdout << --------------------- Uploaded file: four_human_proteins.fasta , ftype: fasta , extra: {'ftype': 'fasta', 'value': 'four_human_proteins.fasta', 'children': []} Uploaded file: blastp_four_human_vs_rhodopsin.tabular , ftype: tabular , extra: {'ftype': 'tabular', 'value': 'blastp_four_human_vs_rhodopsin.tabular', 'children': []} form 'tool_form' contains the following controls ( note the values ) control 0: <HiddenControl(tool_id=fasta_filter_by_id) (readonly)> control 1: <HiddenControl(tool_state=800255c1626362313139396662383639346664316133316565303361646336323163663764636566333538623a376232323566356637303631363736353566356632323361323033303263323032323639366537303735373435663636363137333734363132323361323032323331323232633230323236333666366337353664366537333232336132303232366537353663366332323263323032323639366537303735373435663734363136323735366336313732323233613230323233323232376471002e) (readonly)> control 2: <SelectControl(input_fasta=[*1])> control 3: <SelectControl(input_tabular=[*2])> control 4: <SelectControl(columns=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12])> control 5: <SubmitControl(runtool_btn=Execute) (readonly)> page_inputs (0) {'input_fasta': ['four_human_proteins.fasta'], 'columns': ['1'], 'input_tabular': ['blastp_four_human_vs_rhodopsin.tabular']} --------------------- >> end captured stdout << ---------------------- -------------------- >> begin captured logging << -------------------- galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.jobs: DEBUG: dispatching job 1 to local runner galaxy.jobs: INFO: job 1 dispatched galaxy.jobs.runners.local: DEBUG: executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs.runners.local: DEBUG: execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs: DEBUG: job 1 ended galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2 galaxy.jobs: DEBUG: dispatching job 2 to local runner galaxy.jobs: INFO: job 2 dispatched galaxy.jobs.runners.local: DEBUG: executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs.runners.local: DEBUG: execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs: DEBUG: job 2 ended base.twilltestcase: DEBUG: In submit_form, continuing, but caught exception: cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control base.twilltestcase: DEBUG: ## files diff on /home/pjcock/repositories/galaxy-central/test-data/four_human_proteins_filter_a.fasta and /tmp/tmpijWxYGfour_human_proteins_filter_a.fasta lines_diff=0, found diff = 61 --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 21.504s FAILED (failures=1) functional_tests.py INFO 2010-11-23 13:59:54,494 Shutting down functional_tests.py INFO 2010-11-23 13:59:54,494 Shutting down embedded web server functional_tests.py INFO 2010-11-23 13:59:54,497 Embedded web server stopped functional_tests.py INFO 2010-11-23 13:59:54,497 Shutting down app galaxy.jobs INFO 2010-11-23 13:59:54,497 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:54,498 job queue stopped galaxy.jobs.runners.local INFO 2010-11-23 13:59:54,498 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2010-11-23 13:59:54,498 local job runner stopped galaxy.jobs INFO 2010-11-23 13:59:54,499 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:54,499 job stopper stopped functional_tests.py INFO 2010-11-23 13:59:54,499 Embedded Universe application stopped functional_tests.py INFO 2010-11-23 13:59:54,500 Cleaning up temporary files in /tmp/tmpu4uu_o galaxy.jobs INFO 2010-11-23 13:59:55,410 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:55,411 job queue stopped galaxy.jobs.runners.local INFO 2010-11-23 13:59:55,411 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2010-11-23 13:59:55,411 local job runner stopped galaxy.jobs INFO 2010-11-23 13:59:55,411 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:55,412 job stopper stopped 'run_functional_tests.sh help' for help Note: galaxy test framework uses tool_conf.xml.sample, not tool_conf.xml

2 3

Tabular file metadata - columns names
by Peter 22 Feb '13

22 Feb '13

Hi all, I'd like to know more about Galaxy's column metadata for tabular files. In the workflow editor under "Edit Step Actions" you can pick "Assign Columns", and then give column numbers for five predefined cases: Chrom, Start, End, Strand, Name. Do these "named columns" get shown anywhere in the Galaxy UI? For example, in a column select parameter widget? Is it possible to assign these columns in a tool's wrapper XML file? >From http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I'm aware of the metadata_source attribute to *copy* the meta data from the input file, but that isn't always relevant. Can I somehow specify that my tool has tabular output where column 1 is "Name"? Is it possible to introduce additional column types? e.g. "evalue" or "Description". Thanks, Peter

3 7

run_functional_tests.sh -sid option
by Peter 11 Feb '13

11 Feb '13

Hi, I'm trying to use run_functional_tests.sh to run all the tests for a section (group of tools). I've read the output from: ./run_functional_tests.sh help For example, from the tools_conf.xml.sample we have <section name="ENCODE Tools" id="EncodeTools"> <tool file="encode/gencode_partition.xml" /> <tool file="encode/random_intervals.xml" /> </section> And looking at these tools' XML files, <tool id="gencode_partition1" name="Gencode Partition"> and: <tool id="random_intervals1" name="Random Intervals"> I'd like to run the functional tests for the ENCODE tools, Using the switch for an individual tool id (-id) works, ./run_functional_tests.sh -id gencode_partition1 ... Ran 1 test in 22.302s ... and so does this (well, it say the tool doesn't have any tests which is true in this example): ./run_functional_tests.sh -id random_intervals1 ... Ran 1 test in 0.027s ... However, I also tried using the section id switch (-sid), ./run_functional_tests.sh -sid EncodeTools ... Ran 0 tests in 0.000s ... I also tried using the section name, /run_functional_tests.sh -sid "ENCODE Tools" Is this (-sid not working) a known issue, or am I using it wrong? Thanks, Peter

4 5

Hiding a tool via tool_conf.xml
by Peter Cock 30 Oct '12

30 Oct '12

Hi all, I'm aware that in an individual tool's XML wrapper you can add hidden="true" to the <tool> element to hide the tool from the listing shown in Galaxy's left hand panel (but the tool is still loaded and can be called by old workflows etc). Can this be done via the tool_conf.xml file as well? This would seem useful from a system configuration point of view where it seems wrong to edit the tool wrappers themselves. In fact, it might also be nice to add hidden="true" support to <section> as well as <tool> in tool_conf.xml - although I'm not so sure how useful that would be. Peter

1 2

Re: [galaxy-dev] Inquiring
by Nate Coraor 08 Nov '11

08 Nov '11

Hi Yan, I've again moved this back to the galaxy-dev list. Please reply to this list and not galaxy-user. Yan Luo wrote: > Dear Nate, > > Thanks for your quick response. I appreciate, it is very important for us to > use it. We have problem recently. > > (1) In fact, I can't find the file "paster.log". The problem is that > recently we expanded our gluster(Linux sever) and did the rebalance that has > some bugs. Some of files permission have been changed. So we can't use > User/register righr now, when we tried, we got the sever error, do you have > any idea how to fix it? (we can change the ownships/read and write > permission for some files manually, but we don't know which files and where > they are?) If you are executing run.sh without the --daemon flag, the output will go to whatever terminal window you started Galaxy in, not to a file. You'll want to make sure that all of the files under Galaxy's root directory are owned by a single user, which is the same user which starts and runs the Galaxy process. > (2) We want to reboot the Galaxy, should we first stop and start as > follows? > $ sh run.sh --stop > $ sh run.sh The full command to stop would be `sh run.sh --stop-daemon`, but that only applies if you originally started Galaxy with `run.sh --daemon`. > Is there any difference if I use "-daemon" flag? Last times, my colleague > started using "./run.sh". How to stop it? > If "$ sh run.sh --stop" doesn't work (I didn't try yet, ), how can I find > the process (Linux) that is running by Galaxy and kill it? The --daemon flag runs Galaxy in the background and redirects its output to paster.log. Without the --daemon flag, the process stays connected to the terminal in which you start it. Since Galaxy wasn't originally started with the --daemon flag, you'll need to find the process, either by locating the terminal window in which it was started (possibly by your colleague) and then hitting Ctrl-C, or by using the `ps` command (e.g. `ps auxwww | grep python`) and killing the Galaxy process. It usually looks something like: nate 18213 0.9 0.4 438844 146260 pts/7 Sl+ 10:47 2:30 python ./scripts/paster.py serve universe_wsgi.ini So you would do: % kill 18213 > (3) Could you please let me know if there is a default administrator > user/password for galaxy. I want to add an administrator user, how can I do > that? > According to the instruction, I will change a line of "universe_wsgi.ini" as > follows. How can I set/get my password? > admin_users = yan.luo(a)email.com There is no default. Any users set in admin_uesrs will be administrators. If the account specified in admin_users does not yet exist, you can simply create it. Once created, that account will be an administrator. > (4) I found our "universe_wsgi.ini" contains the following setting, should I > remove "#" before this line, stop and start galaxy? > #allow_user_creation = True No, True is the default setting so with it commented it is still set to True. > I plan to restart our galaxy, if it is possible, could you please let me > know your phone #? I can call you sometime today, or if you prefer, I can > give you my phone #. Unfortunately, we don't have the resources for phone support. We'll be happy to help via email as much as possible. --nate > > Looking forward to hearing from you. > > Best Wishes, > > Yan Luo, Ph.D. > NIH > > > On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > > > Hi Yan, > > > > I've moved this discussion to the galaxy-dev list since it pertains to a > > local installation of Galaxy. > > > > Responses to your questions follow, in-line. > > > > Yan Luo wrote: > > > Dear Sir, > > > > > > (1)We installed Galaxy, but recently the user can't registered and got > > the > > > following error, how can we fix it? > > > > > > Sever error > > > An error occurred. See the error logs for more information.(To turn debug > > on > > > to display ...). > > > > Since debug = False in universe_wsgi.ini, you should be able to find a > > more detailed error message in the log file. If starting Galaxy with: > > > > % sh run.sh --daemon > > > > The default log file is 'paster.log' in Galaxy's root directory. > > > > > (2) Could you please let me know if there is any command to stop galaxy? > > > > If starting with the --daemon flag (as above), you can use: > > > > % sh run.sh --stop-daemon > > > > If running in the foreground, you can use Ctrl-C to terminate the > > process. There is a recent bug whereby Ctrl-C is ineffective on some > > platforms under Python 2.6 - in this case you will have to kill/pkill > > the process manually. We are working on a fix for the latter. > > > > > (3) If I reset universe_wsgi.ini file and want to set an administrator > > > user(I can add a line in the above file), how can I get the password? > > Should > > > I stop galaxy(See question 2) first? then run "./setup.sh" and > > "./run.sh". > > > > setup.sh would have only been necessary prior to running Galaxy the > > first time, however, this step has recently been removed. If you are > > referencing documentation that still refers to setup.sh, please let us > > know so we can update it - I did notice this was still on the > > "Production Server" page, so I removed it from there. > > > > You no longer need to run setup.sh at all. > > > > > (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be > > generated? > > > if I want to change this file,should I edit it before "run.sh" and after > > > "setup.sh". Is it right? > > > > setup.sh and its replacements in run.sh and the Galaxy application > > itself never overwrite files, they only create files from sample files > > if they do not exist. > > > > > (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and > > > "./setup.sh"(./run.sh), which one is correct under Linux? > > > > Both syntaxes are effectively the same in most cases. > > > > --nate > > > > > > > > Looking forward to hearing from you. > > > > > > Best Wises, > > > > > > Yan Luo, Ph.D. > > > NIH > > > < > > http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way, > > > > > > > > _______________________________________________ > > > galaxy-user mailing list > > > galaxy-user(a)lists.bx.psu.edu > > > http://lists.bx.psu.edu/listinfo/galaxy-user > > > >

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Automatically removing items from history
by Kempenaar, M (med) 08 Sep '11

08 Sep '11

Hello, Is it possible to let a tool in a workflow manage the users history? For instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file. I was hoping that when I remove a file from disk that it would also be removed from the history, but that only results in a 'The resource could not be found.' error. Alternatively, is it possible to create a composite datafile/history item from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier. (this is a bit of a followup for: http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-number…) One other question, is there (any) documentation available on the Galaxy API or a set of example files? Thanks for your input! Regards, Marcel. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

4 4

plotting/statistics tools suggestion
by Marshall Hampton 13 Jul '11

13 Jul '11

I've just started seriously looking at Galaxy, and I already have a suggestion (everyone's a critic...): switch from using rpy or even rpy2 to scipy/numpy/matplotlib for basic statistics and plots. I wrestled a bit with getting rpy to work on my local setup and decided it would be quicker to write my own plotting tool extensions, which indeed turned out to be the case. Since you already require python it seems much more natural to use python-native tools. To give some positive feedback, learning to write an extension was surprisingly easy and encourages me to work on more. I use currently use Sage (http://www.sagemath.org/) to both analyze next-generation sequence data (454 and Illumina) and create interactive tools for the biologists I collaborate with. The Sage project involves many of the same issues and challenges facing Galaxy. Sage is based on python, but includes R. I realize that there are many things you would want to do with R that aren't included in scipy/biopython, so it might be worthwhile to look at how Sage wraps R. Its far from perfect, but I prefer it to rpy2. In the Sage source tree the interface is at: $SAGE_ROOT/devel/sage/sage/interfaces/r.py. (Ugly online copy at: http://hg.sagemath.org/sage-main/file/361a4ad7d52c/sage/interfaces/r.py) -Marshall Hampton Department of Mathematics and Statistics and the Integrated Biosciences Program University of Minnesota Duluth

2 1

importing annotation with dataset
by Davide Cittaro 01 Jul '11

01 Jul '11

Hi, is it just me or when I try to import a dataset from a library to a history, annotation is not retained (whereas "info" is)? d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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