August 2012 - galaxy-dev - lists.galaxyproject.org

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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Some questions about histories
by Sascha Kastens 16 Aug '12

16 Aug '12

Hi all! I have two questions about histories in Galaxy: 1. Is it possible to mark/set a history as published via the API? 2. How can I get the ID of the current users history via a tool? Something like ${__app__.model.User.get($__user_id__).histories[0].id} ?! Thanks in advance! Cheers, Sascha

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Re: [galaxy-dev] Conditionally showing certain form elements on tool page
by Dan Tenenbaum 15 Aug '12

15 Aug '12

Hi John, On Wed, Aug 15, 2012 at 7:32 PM, 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, > > This page really helped me understand how the tags worked as well as looking > at some older tools: > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Thanks for the pointer. I have seen this page, but I'm still stuck. I'll read it again more carefully though. > > I will take a look at my tool when I get to the office tomorrow. Thanks. I appreciate it! 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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Another trackster issue?
by SHAUN WEBB 15 Aug '12

15 Aug '12

I am looking at bigwig files in trackster. When I zoom in the point where 20kb is displayed on screen I get large blocks of the track separated by empty gaps. When I zoom in to these gaps there is definitely track signal there. Is this a bug or is this intended to limit the amount of data to load? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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refresh user history
by Quang Trinh 15 Aug '12

15 Aug '12

Hi dev, We have a script that download a number of files from an external site, however, only the first file shows up in the user history once the downloads are complete. The rest of the files show up when we click on the refresh user history button. Is there a way to refresh the user history in our script when all the files are downloaded? THanks, Q

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