user specific access/options
by Jennifer Jackson
Hi Petr,
I am going to forward your email to the galaxy-dev list so that the
development community can offer comments/suggestions.
Best,
Jen
Galaxy team
On 8/30/11 2:27 AM, Petr Novak wrote:
> Hi everybody,
> I am developing the application on Galaxy server. One of the requirement
> is to create user specific list of options. Is it possible to access
> somehow $__user_email__ in <options> tag or in <conditional> ?. I did
> not found documentation how to used cheetah in galaxy tool xml files but
> from files provided with galaxy, cheetah is used only in <command> and
> <config> tag. Is that rigth? If it can be used in any part of xml
> definition file it would make much easier to generate xml dynamicaly
> based on the $__user_email__
> Does anybody have an idea how to manage this problem?
> Petr Novak
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
5 years, 3 months
Default value for data_column not working?
by Peter Cock
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
5 years, 4 months
Re: [galaxy-dev] [galaxy-user] Inquiring
by Nate Coraor
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
5 years, 10 months
Puzzling test failure with data_column parameter
by Peter Cock
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
6 years, 4 months
Tabular file metadata - columns names
by Peter
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
6 years, 6 months
run_functional_tests.sh -sid option
by Peter
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
6 years, 7 months
Problems with Internet Explorer 9?
by Peter Cock
Hello all,
Are there (or were there) any known problems with Galaxy under
Microsoft Internet Explorer 9? One of our biologists is now having
problems with our local Galaxy server, probably after updating his
browser.
Specifically new history entries do not seem to automatically update
from queued to running to done, and also the "peep" functionality to
expand/collapse a history entry had stopped working. This was on a
large history of about 100 entries.
We installed Firefox 10, logged into Galaxy, and it was fine with this
same history.
A quick test on the public Galaxy with a single history entry seemed
to work in both browsers, so perhaps this is something you've already
fixed in the latest Galaxy - or perhaps it depends on the size of the
history.
Any ideas? Has anyone else seen something similar?
Thanks,
Peter
6 years, 9 months
producing HTML output with images
by Nikhil Joshi
Hi all,
I am having trouble producing HTML output with images. In the past I
have been able to produce HTML files with no images and it seemed to
work fine. However, now I am writing a script that produces
diagnostic images and I want to display all of the images on one page
using HTML. I am using the "files_path" variable to create the plots
in the working directory, and then I am using the "extra_files_path"
variable to access the final plot from the html file. I look at the
resulting HTML files and it points to the proper plot full path, and
the plot DOES exist... but when I click to view the output, the plot
doesn't render. It just shows an empty box with a "broken image"
icon, however, the text does render. I copy the plot file, and I can
view it fine by itself. I copy the plot and the html and I can view
the page just fine offline, but galaxy doesn't want to render the
image for some reason. What am I doing wrong?
- Nik.
--
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
Davis, CA
6 years, 9 months
Hiding a tool via tool_conf.xml
by Peter Cock
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
6 years, 10 months
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
by TerAvest, Emily
Hi Leandro,
I am also experiencing the same problem with the latest version of galaxy. I just attempted to connect our sequencer for the first time yesterday. I do not have an older version of galaxy to test and compare to see if it works in earlier versions. I am able to transfer data from the sequence to the import directory, however it is not moved to the data library. My data_transfer.log also has the same error.
"The server could not comply with the request since it is either malformed or otherwise incorrect."
Does anyone have a solution for this?
Thanks
Emily
------------------------------
Message: 17
Date: Wed, 28 Mar 2012 13:15:47 +0200
From: Leandro Hermida <softdev(a)leandrohermida.com>
To: Luobin Yang <yangluob(a)isu.edu>
Cc: Galaxy Dev <galaxy-dev(a)bx.psu.edu>
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
queue" forever
Message-ID:
<CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA(a)mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you <Location
/> ... </Location> container to not match URLs starting with /api. To
do this you have to change it to <LocationMatch "^/(?!api)"> ....
</LocationMatch>.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang <yangluob(a)isu.edu> wrote:
> I've got the same problem and when I looked at the data_transfer.log, I saw
> the following message:
>
> 2012-03-01 15:12:27,338 - datatx_13870 -
> (u'9c17d84742cd2acb63d88b5bd41d968f',
> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
> 'new_status': 'Adding to data library'})
> 2012-03-01 15:12:27,342 - datatx_13870 - Error. <!DOCTYPE HTML PUBLIC
> "-//IETF//DTD HTML 2.0//EN">
> <html><head>
> <title>405 Method Not Allowed</title>
> </head><body>
> <h1>Method Not Allowed</h1>
> <p>The requested method PUT is not allowed for the URL
> /api/samples/2d9035b3fc152403.</p>
> <hr>
>
> Using Galaxy instead of Apache as the web server changed the sample status
> from "in queue" to complete but didn't add the downloaded files to the data
> library.
>
> Luobin
>
> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
> <softdev(a)leandrohermida.com> wrote:
>>
>> Dear Galaxy Dev,
>>
>> I've set up the Galaxy sample tracking system data transfer
>> functionality exactly as specified here
>> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
>> attempt to transfer datasets it puts them into the queue and then
>> never seems to transfer anything.
>>
>> The galaxy_listener.log shows:
>>
>> 2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
>> {'config_file': 'universe_wsgi.ini', 'http_server_section':
>> 'server:main'}
>> 2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
>> 'rabbitmqctl_path':
>>
>> '/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
>> 'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
>> 'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
>> 'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
>> '5672'}
>> 2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
>> 127.0.0.1:5672
>> 2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
>> 2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
>> 2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
>>
>> "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py"
>> " <data_transfer>
>> <galaxy_host>rd-galaxydev.app.pmi</galaxy_host>
>> <api_key>69bbd1a9b18eda2a888e9963820d8ef0</api_key>
>> <data_host>chp723</data_host>
>> <data_user>galaxy</data_user>
>> <data_password>mypassword</data_password>
>> <request_id>12</request_id>
>> <sample_id>12</sample_id>
>> <library_id>15</library_id>
>> <folder_id>52</folder_id> ? ? ? ? ? ? ? ? ? ?<dataset>
>> ?<dataset_id>10</dataset_id>
>> <name>ttt_2.fastq.gz</name>
>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz</file>
>> ? ? ? ? ?</dataset><dataset>
>> <dataset_id>9</dataset_id>
>> <name>ttt_1.fastq.gz</name>
>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz</file>
>> ? ? ? ? ?</dataset> ? ? ? ? ? ? ? ?</data_transfer>"
>> "universe_wsgi.ini"
>>
>> The FASTQ files are for testing and aren't very big (7.6 MB), what
>> could be going wrong?
>>
>> regards,
>> Leandro
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>> and other Galaxy lists, please use the interface at:
>>
>> ?http://lists.bx.psu.edu/
>
>
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