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by ashwinikumar＠utdallas.edu 19 Aug '12

19 Aug '12

MY Y Sent from my iPhone

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pipeline execution succeeds but galaxy shows failure
by Brian Haas 17 Aug '12

17 Aug '12

Hi, I wrote a pipeline (xml attached) that, from what I can gather, succeeds, but galaxy shows it as an error and doesn't make the output file accessible as a new data set. >From the server log, I can see that the command line is being constructed correctly, and it even indicates that it's captured the output, but in the display of the web browser, it just shows up in the error state. The script being run exits (0) on success. Any ideas? Here's what the output section of my xml file looks like: <outputs> <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: coord-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/> </outputs> and here's what the server log states: galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job dispatched galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453 executing: alignReads.pl --target /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat -o alignment --aligner bowtie --single /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat --seqType fq galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam to /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat as directed by from_work_dir Again, as far as I can tell, everything worked - but the browser doesn't think so. I've run the exact command above on the command-line, and it exits(0) indicating success. Also, I've verified that when run through my galaxy instance, the galaxy-relocated output file is as expected. Many thanks for your help. I'm still getting my feet wet with galaxy, reading through all the documentation and searching the mailing list for additional help. best regards, -brian -- -- Brian J. Haas Manager, Genome Annotation and Analysis, Research and Development The Broad Institute http://broad.mit.edu/~bhaas

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TopHat Wrapper to handle Multiple Fastq reads
by Vijaykant N 17 Aug '12

17 Aug '12

Greetings, I was working on the TopHat wrapper (we have customized one for handling just one input Fastq read) for handling multiple reads. I figured out that using repeat tag was the way forward, but have been having a hard time with the Cheetah template. Any help or suggestions? Sincerely, Vijay

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optional="false" not working?
by Dan Tenenbaum 17 Aug '12

17 Aug '12

Hello, I have the following wrapper: <tool id="foo" name="foo" version="0.99.0"> <description>foo</description> <command interpreter="python"> tool.py $outputFileName </command> <inputs> <param name="tp" type="text" label="label" help="help" optional="false"/> </inputs> <outputs> <data format="csv" name="outputFileName"/> </outputs> </tool> I expect that when I click "Execute" I will be told that "tp" must have a value. However, that doesn't happen, it just goes ahead and executes the script. How do I get Galaxy to require that a text param have a value? Thanks, Dan

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Problem installing local instance of Galaxy
by Kenneth Watanabe 17 Aug '12

17 Aug '12

To Galaxy, I installed Galaxy on my local server.. I modified the universe_wsgi.ini file as follows: # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. host = 0.0.0.0 I type the following command at the LINUX prompt to start the service $ sh run.sh ... Starting server in PID 2685 serving on 0.0.0.0:8080 view at http://127.0.0.1:800 When I open FIrefox directly on the server and go to the web address http://localhost:8080 the galaxy screen appears. When I open FIrefox on my PC and go to http://localhost:8080, I get the following error "Unable to connect Firefox can't establish a connection to the server at localhost:8080." Any suggestions would be greatly appreciated. -- Kenneth Watanabe University of Nevada

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Re: [galaxy-dev] Conditionally showing certain form elements on tool page
by Dan Tenenbaum 16 Aug '12

16 Aug '12

Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson <jmpatt4(a)g.uky.edu> wrote: > On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: >> >> Hi all, >> >> I'm trying to wrap my head around what the <conditional> tag does...it >> looks like it doesn't do what I would like. >> >> I want to create a tool that allows the user to upload a data file and >> then have it run through one or more filters. Each filter takes one or >> more parameters. >> >> I was thinking I could do something like this: >> >> >> <inputs> >> <conditional name="mycond"> >> <param name="checktest" type="boolean" label="foo" >> value="yessir"> >> </param> >> <when value="yessir"> >> <param name="param1" type="text" label="bar" value="twunk"> >> </param> >> </when> >> </conditional> >> </inputs> >> >> The idea being, if the user checks the box labeled "foo", a text box >> labeled "bar" will appear. >> And I would have several such checkboxes and their accompanying >> parameters. >> But what I get is just the checkbox, and nothing happens when I click it. >> >> Is it possible to do what I have in mind, and if so, how? >> >> Also note that these conditions are not mutually exclusive. A user can >> select one *or more* filters. So I'm not sure how the body of my >> <command> tag should look. Is there a way I can just pass every >> possible parameter to my script like this: >> myscript.py param1=foo param2=bar >> If a parameter is not defined (because the user didn't click its >> associated checkbox), then the script will receive e.g. >> param1= param2=bar >> but it can deal with that. >> >> I realize I can make several tools and chain them together in a >> workflow, but that seems like overkill for this use case, and it would >> be nice if the user could set up their desired filters on one screen. >> >> Is this possible? >> Thanks! >> Dan >> ___________________________________________________________ >> 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: >> >> http://lists.bx.psu.edu/ > > Hello Dan, > > The easiest way to go about this, since you said that none of your > filters are mutually exclusive, is to use the "select" datatype. I don't > think you even need the conditional tags. Galaxy says that you need <when> > tag sets when you use conditionals, but this is not true, as I have similar > code as I have written below. Use type="select" in your parameter. This > gives you a button that can have a multitude of options, but most of mine > are simply used like booleans. Something like this: > > <inputs> > <param name="param1" type="select" label="filterName" help="helpful > tips"> > <option value="yes">yes</option> > <option value="no">no</option> > </param> > <param name="param2" type="select" label="filter2Name" help="more > helpful tips"> > <option value="yes">yes</option> > <option value="no">no</option> > </param> > </inputs> > > I had certain options that WERE mutually exclusive, and required nested > conditional statements, where I had an outer conditional for the extra > options, and an inner conditional around each parameter. > > As for the command tag, the select type parameters make it easy because you > can just check the string values with an if statement, like so: > (assuming python) > <command interpreter="python"> > tool.py > #if $param1 == "yes": > --YourGetOptFlag > #else: > ##dont even need an else, just ignore > #end if > > </command> > > If I am not mistaken, this should be sufficient if all you need to pass is a > flag indicating your program to use the filter. If you need to pass a flag > AND integer values, you are going to have to wrap your parameters in > conditional tags and use a set of <when>: > > <inputs> > <conditional name="firstConditional"> > <param name="param1" type="select" label="filterName" help="helpful > tips"> > <option value="yes">yes</option> > <option value="no">no</option> > </param> > <when value="yes"> > <param name="IntegerBox" type="integer" value="[default value]" > min="(optional)" max="(optional)" label="UseParamName" help="helpful text" > /> > </when> > <when value="no" />  > </conditional> > </inputs> > > Rinse and repeat, adding conditionals around each select. I think this is > actually what you want to do, as you say you want a box to appear after a > user selects whether or not to use the filter. Also, quick note, the text > between the option tags are what appear on the select buttons, so they can > be whatever you want. The value="" is the important thing, as this is what > you will evaluate the "if/else" to in the <command> tag. One last thing, The > cheetah command is really no different. > > <command interpreter="python"> > tool.py > #if $firstConditional.param1 == "yes": > --testGetOpt $firstConditional.IntegerBox > #end if > > </command> > > The second command tag is how I pass a few parameters into my command line > tool. > > > Anyway, I hope this helped a little bit. If you need anything else, let me > know and I will see If I can help. A lot of this was trial and error and I > am sure there are trickier ways to doing it, but this worked for the scope > of my program. > This is extremely helpful! Thanks. I find the select box yes/no idiom a bit awkward. I'd prefer a checkbox (just a single one, not one each for "yes" and "no") but doing a select box is ok too, I can live with that. I'm running into problems constructing my command, though. I'm new to cheetah so that might be it. First off, here's my inputs and outputs: <inputs> <conditional name="firstConditional"> <param name="param1" type="select" label="Filter 1" help="helpful tips"> <option value="no">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="IntegerBox" type="integer" value="1" min="0" max="5" label="A parameter to filter 1" help="helpful text" /> </when> <when value="no" />  </conditional> <conditional name="secondConditional"> <param name="param2" type="select" label="Filter 2" help="helpful tips"> <option value="no">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="IntegerBox2" type="integer" value="1" min="0" max="5" label="A parameter to filter 2" help="helpful text" /> </when> <when value="no" />  </conditional> </inputs> <outputs> <data format="csv" name="outputFileName"/> </outputs> So the page displays two select boxes. If you select either one of them, a text box appears. This feeds to a python script that for now just echoes the parameters passed in and writes them to a file, which I can examine in galaxy. So here is what I have in the command section: <command interpreter="python"> tool.py #if $firstConditional.param1 == "yes": --filter1 $firstConditional.IntegerBox #end if # if $secondConditional.param2 == "yes": --filter2 $secondConditional.IntegerBox2 #end if $outputFileName </command> This results in an error: galaxy.jobs.runners.local ERROR 2012-08-16 10:43:42,677 failure running job 87 Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job job_wrapper.prepare() File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/__init__.py", line 429, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1971, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1244, in __init__ self._compile(source, file, compilerSettings=compilerSettings) File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1538, in _compile keepRefToGeneratedCode=True) File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 745, in compile compiler.compile() File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Compiler.py", line 1670, in compile self._parser.parse() File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Parser.py", line 1488, in parse self.eatDirective() File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Parser.py", line 1610, in eatDirective directiveParser() File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Parser.py", line 1761, in eatEndDirective self.popFromOpenDirectivesStack(directiveName) File "/Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Parser.py", line 2645, in popFromOpenDirectivesStack raise ParseError(self, msg="#end found, but nothing to end") ParseError: #end found, but nothing to end Line 8, column 1 Line|Cheetah Code ----|------------------------------------------------------------- 5 | # if $secondConditional.param2 == "yes": 6 | --filter2 $secondConditional.IntegerBox2 7 | #end if 8 | $outputFileName ^ 9 | What I am trying to do is build up a command line bit by bit. Pseudocode would be like this: commandline = "tool.py " if condition_a: commandline += "--filter1 25.6 " if condition_b: commandline += "--filter2 86.2 " commandline += "outputfilename" What am I doing wrong? Thanks again! Dan > -John > > > > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/

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Parameter tracking in workflows
by Jonathan Manning 16 Aug '12

16 Aug '12

Hello all, I have a set of galaxyised R scripts, called directly via 'Rscript', which I run in workflows for microarray analysis. I would like to collect the parameters used at each step, for report generation, re-runs and provenance. My Galaxy noob instincts tell me to have each script 'output its inputs' to a file, several of which I would collate at the end of the workflow. Is there, as I suspect, a better way of doing this? I'm sure Galaxy has the info somewhere, I'm just not sure how to get at and use it. Is there a global variable I can pass from the tool xml that can be used to access this info? All pointers appreciated. Thanks, Jon -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Conditionally showing certain form elements on tool page
by Dan Tenenbaum 16 Aug '12

16 Aug '12

Hi all, I'm trying to wrap my head around what the <conditional> tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: <inputs> <conditional name="mycond"> <param name="checktest" type="boolean" label="foo" value="yessir"> </param> <when value="yessir"> <param name="param1" type="text" label="bar" value="twunk"> </param> </when> </conditional> </inputs> The idea being, if the user checks the box labeled "foo", a text box labeled "bar" will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my <command> tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan

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Problem with "upload file" tool on file uploaded through FTP server
by Sarah Diehl 16 Aug '12

16 Aug '12

Hi everyone, my local installation of Galaxy has an issue with using the "Upload File" tool on data that was uploaded to the ftp server. The ftp upload itself works fine: -rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa but there seems to be some issue with Galaxy moving it and I have no clue where the problem is. The final dataset /galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a file, but empty: -rw-rw-r--. 1 galaxy galaxy 0 2012-08-16 13:53 dataset_24020.dat I'm grateful for any hints. Best regards, Sarah ----- Forwarded Message ----- From: diehl(a)immunbio.mpg.de To: diehl(a)immunbio.mpg.de, diehl(a)immunbio.mpg.de Sent: Thursday, August 16, 2012 1:55:04 PM Subject: Galaxy tool error report from diehl(a)immunbio.mpg.de GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "xxx" ----------------------------------------------------------------------------- This is in reference to dataset id 24020 from history id 1393 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 115: 28S_rRNA.fa by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. xxx ----------------------------------------------------------------------------- The user 'diehl(a)immunbio.mpg.de' provided the following information: ----------------------------------------------------------------------------- job id: 20566 tool id: upload1 ----------------------------------------------------------------------------- job command line: python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server /galaxy/galaxy_server/database/tmp/tmpw_TcHa /galaxy/galaxy_server/database/tmp/tmpKwHCcx 24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/galaxy/galaxy_server/tools/data_source/upload.py", line 403, in <module> __main__() File "/galaxy/galaxy_server/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/galaxy/galaxy_server/tools/data_source/upload.py", line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py", line 98, in convert_newlines shutil.move( temp_name, fname ) File "/usr/local/lib/python2.7/shutil.py", line 299, in move copy2(src, real_dst) File "/usr/local/lib/python2.7/shutil.py", line 129, in copy2 copystat(src, dst) File "/usr/local/lib/python2.7/shutil.py", line 98, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/galaxy/galaxy_server/database/ftp/diehl(a)immunbio.mpg.de/28S_rRNA.fa' ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

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Re: [galaxy-dev] how to edit attributes of tool
by Robert Chase 16 Aug '12

16 Aug '12

Yes:) I meant to do it algorithmically though from within the code of the tool or the xml wrapper:) On Wed, Aug 15, 2012 at 7:10 PM, Ross <ross.lazarus(a)gmail.com> wrote: > Does clicking the info (i) icon on a history item help? > > > On Wed, Aug 15, 2012 at 7:16 AM, Robert Chase <rerpc(a)channing.harvard.edu>wrote: > >> Hello, >> >> Is there a way to annotate the notes of a custom tool to include >> information about the parameters passed to the tool? Let us say a user >> specifies a number n as a parameter to the tool. Is it possible to put this >> parameter in the notes that appear when the pencil icon is pressed? >> >> Reading the notes under the <data> tag set, >> >> wiki.g2.bx.psu.edu/Admin/Tools/Tool Config Syntax >> >> I didn't see any hint about how to pass the script parameters to the >> metadata boxes under the pencil icon. >> >> -Rob >> >> ___________________________________________________________ >> 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: >> >> http://lists.bx.psu.edu/ >> > > > > -- > Ross Lazarus MBBS MPH; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 > http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ >

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