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Apache proxy configuration
by sohkhan＠notes.cc.sunysb.edu 23 Aug '10

23 Aug '10

Hi I installed Galaxy on Mac OS 10.6.4, everything was working fine until I tried to use Apache server. I followed the directions as per http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. Added the following to my httpd.cof RewriteEngine on <Location "/"> # Define the authentication method AuthType Basic AuthName Galaxy AuthUserFile /home/nate/htpasswd Require valid-user # Define Galaxy as a valid Proxy <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e </Location> RewriteRule ^/static/style/(.*) /home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /home/nate/galaxy_dist/static/$1 [L] RewriteRule ^/favicon.ico /home/nate/galaxy_dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/nate/galaxy_dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] </Location> I am getting a "<Proxy not allowed here" error where I start apache. Any help is appreciated. -Sohail

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Galaxy Tool Shed now allows you to rate and review tools
by Greg Von Kuster 20 Aug '10

20 Aug '10

Hello Galaxy Community, The Galaxy Tool Shed at http://usegalaxy.org/community now allows you to rate and review tools contributed by others. Please keep sharing your tools - doing so provides a significant benefit to the community! Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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August 20, 2010 Galaxy Development News Brief
by Greg Von Kuster 20 Aug '10

20 Aug '10

The latest news brief is available at the following link. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Two questions: Daemon (no error code returned) and access configuration arguments
by padioleau 20 Aug '10

20 Aug '10

Dear Galaxy developers, I have two questions: First, when Galaxy is launched in daemon mode, there is no error returned if Galaxy does not start properly. For instance if the database needs to be updated, the daemon will succeed (no error code is returned) even though Galaxy is not started. I would like to know if it is possible to change that. Second, and for something completely different, I would like to know how I can get within a tool wrapper access to Galaxy configuration arguments like 'new_file_path' for example. Thanks, Ismael -- Padioleau Ismael EMBL Heidelberg ( V205)

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Re: [galaxy-dev] [galaxy-user] why is ./tools/sr_mapping/bowtie_color_wrapper.xml not implemented by default?
by Kelly Vincent 20 Aug '10

20 Aug '10

Kevin, Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup) which details how to set these up. Let us know if you need further information. (Note that this topic is better suited to galaxy-dev instead of galaxy- user since it's about local installations.) Regards, Kelly Galaxy Team On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote: > Hi, > I see that the public galaxy at usegalaxy.org > has a few differences with a local installation in that some tools > are not implemented as well. > for e.g. > ./tools/sr_mapping/bowtie_color_wrapper.xml > > May I know if there's a reason for this? > > Cheers > Kevin > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: [galaxy-dev] Dataset generation errors
by Branden Timm 19 Aug '10

19 Aug '10

Hey Ryan, Thanks for the tip, redirecting to /dev/null works but then I lose the script output that used to be visible in the history (dataset generation still works fine). Trying to redirect stderr to stdout, using 2>&1, seems to cause a parse error in my .xml configuration file. The line: <command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1 </command> Causes my tool not to show up under the tools section at all. Cheers -Branden On 8/19/2010 9:48 AM, Ry4an Brase wrote: > On Thu, Aug 19, 2010 at 09:34:40AM -0500, Branden Timm wrote: >> Hi All, >> I have been working to integrate SOAPaligner/soap2 into my Galaxy >> instance, and now have it mostly working thanks to some good advice from >> this list. However when I execute my tool, the history item for the >> resulting dataset turns red and says an error occured while running the >> job. When I look at the error message, it is simply the output of the >> soap2 tool, as follows: >> Begin Program SOAPaligner/soap2 > [snip] >> So why is Galaxy thinking there was an error generating the dataset? Do I >> have to suppress output from soap2 using a wrapper? > Galaxy will consider the job to have errored out if any text was output > to the STDERR file handle. Output to STDOUT file handle is okay and is > saved. > > See this one for more details: > > http://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-… > > If your output is correct using > > jobcommand ARGS 2>&1 > > or > > jobcommand ARGS 2>/dev/null > > should get you there. > >

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Dataset generation errors
by Branden Timm 19 Aug '10

19 Aug '10

Hi All, I have been working to integrate SOAPaligner/soap2 into my Galaxy instance, and now have it mostly working thanks to some good advice from this list. However when I execute my tool, the history item for the resulting dataset turns red and says an error occured while running the job. When I look at the error message, it is simply the output of the soap2 tool, as follows: Begin Program SOAPaligner/soap2 Thu Aug 19 09:27:43 2010 Reference: /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index Query File a: /home/galaxy/galaxy_dist/database/files/000/dataset_150.dat Output File: /home/galaxy/galaxy_dist/database/files/000/dataset_151.dat Load Index Table ... Load Index Table OK Begin Alignment ... 131072 ok 0.46 sec 262144 ok 0.43 sec 393216 ok 0.44 sec 524288 ok 0.45 sec 655360 ok 0.44 sec 702613 ok 0.19 sec Total Reads: 702613 Alignment: 672995 (95.78%) Total Elapsed Time: 5.03 - Load Index Table: 0.48 - Alignment: 4.55 SOAPaligner/soap2 End Thu Aug 19 09:27:48 2010 Additionally, the resulting dataset is a correct, and I can view it by clicking on the eye icon for that history item. I've also taken the exact command from paster.log and run it as the galaxy user, and the script does have a 0 return code. So why is Galaxy thinking there was an error generating the dataset? Do I have to suppress output from soap2 using a wrapper? Cheers -- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm(a)glbrc.wisc.edu

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Fwd: [galaxy-user] Tool Integration: SOAPaligner/soap2
by Kelly Vincent 18 Aug '10

18 Aug '10

Begin forwarded message: > From: Kelly Vincent <kpvincent(a)bx.psu.edu> > Date: August 18, 2010 11:46:32 AM EDT > To: btimm(a)wisc.edu > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] [galaxy-dev] Tool Integration: > SOAPaligner/soap2 > > Branden, > > Are you currently calling a script file (Python Perl, etc.) in your > command tag, or calling the tool directly? If you are running it > only with an XML file, you cannot do what you want here. The command > that will be run is generated by converting the variable values you > put in the <command> tag to the names of the actual input and output > files that Galaxy creates when the tool is run. > > However, this is not particularly difficult if you are calling a > script in the <command> tag, though it's a little convoluted. There > are several tools that deal with this situation (the NGS tools > again, in particular). There are a couple of basic situations. If > you just need to have a single file with a certain extension, simply > create a temp file with the extension specified (in Python > "tempfile.mkstemp( suffix='.ext' )" will do it). It's slightly more > complicated if you need associated files in the same directory (for > instance, Samtools expects a fasta file like "hg19.fa" plus its > index "hg19.fa.fai" to be in the same place. When you call the > indexing command with the name of the fasta file, it automatically > creates the index file with that name plus ".fai"). In this case, > you should symlink the original file to a temp file (with or without > a specified extension, as appropriate) and then get the name of that > temp file. The name of the other file is that name PLUS the > appropriate extension. For example, sam_to_bam.py does this in lines > 73 through 76. > > Note that the reason for symlinking to a temp file is that otherwise > the tool will create a new file in a database/files subdirectory, > which is not the right way to do things. So in the Samtools case, if > the uploaded fasta file is "database/files/000/dataset_23.dat", a > new file "database/files/000/dataset_23.dat.fai" will be created, > but the database won't know about it and it will not be deleted > after the tool finishes (but it still won't be available to future > use, either). > > The paster.log contains the command as generated by the <command> > tag, but it's not possible to print to that log from a tool script. > You can simply print the relevant command to sdtout or stderr from > the script and when you run it in the browser, you will see it in > the info section. > > Hopefully this makes sense--let us know if you need further > assistance. > > Regards, > Kelly > > > On Aug 17, 2010, at 1:21 PM, Branden Timm wrote: > >> Just a follow up here ... if the <command> tag needs to list all >> output files, but the tool itself does not specify output files on >> the command line, does that mean I need to write a wrapper for my >> tool that accepts each output file as a command-line parameter? >> >> Currently I've tried specifying all of the output files on the >> <command> line, where each variable corresponds to a <data> line >> under outputs, but then SOAPaligner/soap2 tries to read those non- >> existent files as FASTA files. >> >> As a more general question, is there a way to see the exact >> command(s) that Galaxy is dispatching on my behalf when I execute a >> tool? I checked paster.log but it wasn't there. It seems like >> that would be a great debugging feature. >> >> Branden >> >> On Aug 17, 2010, at 10:06 AM, Hans-Rudolf Hotz wrote: >> >>> Hi Branden >>> >>>> Hello, >>>> I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a >>>> test >>>> integration case. >>>> >>>> soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder >>>> takes a FASTA files and generates a set of 13 different index >>>> files, >>>> which soap needs in order to do it's alignment. >>>> >>>> I have started by just creating the tool XML configuration for >>>> 2bwt-builder. The configuration follows: >>>> >>>> <tool id="2bwt-builder" name="2bwt-Builder"> >>>> <description>build index files for the SOAPaligner/soap2</ >>>> description> >>>> <command>2bwt-builder $input</command> >>> >>> the "command line" needs all output files listed, see: >>> http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial >>> >>> >>> However, in your case: Do you really want to make an extra tool >>> for the indexing step? Wouldn't it make more sense to have the >>> indices pre-built for some genomes? >>> >>> Your soap galaxy tool can then re-use the indices again and again. >>> This is also much more space efficient, as all the user share the >>> same index files. >>> >>> Regards, Hans >>> >>> >>>> <inputs> >>>> <param type="data" format="fasta" name="input" label="Source >>>> file"/> >>>> </inputs> >>>> >>>> <outputs> >>>> <data format="tabular" name=".amb Index File"/> >>>> <data format="tabular" name=".ann Index File"/> >>>> <data format="tabular" name=".bwt Index File"/> >>>> <data format="tabular" name=".fmv Index File"/> >>>> <data format="tabular" name=".hot Index File"/> >>>> <data format="tabular" name=".lkt Index File"/> >>>> <data format="tabular" name=".pac Index File"/> >>>> <data format="tabular" name=".rev.bwt Index File"/> >>>> <data format="tabular" name=".rev.fmv Index File"/> >>>> <data format="tabular" name=".rev.lkt Index File"/> >>>> <data format="tabular" name=".rev.pac Index File"/> >>>> <data format="tabular" name=".sa Index File"/> >>>> <data format="tabular" name=".sai Index File"/> >>>> </outputs> >>>> </tool> >>>> >>>> I've used the tabular data type for the output files, which I'm >>>> not sure >>>> is correct. When the script runs, it generates 13 output files in >>>> my >>>> history, but they are all empty according to galaxy. When I look at >>>> galaxy_dist/database/files/.../, the output files have been >>>> generated >>>> correctly and are non-empty. >>>> >>>> Where am I going wrong? Thank you in advance for any advice. >>>> >>>> -- >>>> Branden Timm >>>> System Administrator >>>> Great Lakes Bioenergy Research Center >>>> University of Wisconsin >>>> btimm(a)glbrc.wisc.edu >>>> _______________________________________________ >>>> galaxy-dev mailing list >>>> galaxy-dev(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Writing a tool, need wisdom on <output>
by Reid, Robert 17 Aug '10

17 Aug '10

Hi, We have begun dabbling with a local instance of Galaxy (amazingly impressive !!). I have 2 questions: 1. I have written a tool to implement Lucy (http://bioinformatics.oxfordjournals.org/cgi/content/short/17/12/1093) I can figure out how to handle output when the command line has a -o option to explicitly state the output file name. Or when the file output is always the same. I am trying to make a tool where the java executable is launched and makes an output file. The output file is named the same as the input file (input.txt) but has a new extension added to the end of it (.cal), i.e., inputfilename.txt.cal I can't for the life of me figure out the XML syntax to read this file back into galaxy as an output. Is the best strategy to write a wrapper in another language (perl, python, java), that will feed in $output, then read in the ".cal" output and spew out a file to satisfy $output for the XML ? 2. For testing, what is the best way to do the testing? I have written a few java based executable jars and the corresponding XML docs to go with them. I'd like to share with the world but I am not sure the best way to go testing. Thank you very much for your attention, Rob Reid Rob Reid, Ph.D. | Research Associate UNC Charlotte | Dept. of Bioinformatics and Genomics 9201 University City Blvd. | Charlotte, NC 28223 Phone: 704-250-5766 rreid2(a)uncc.edu | http://www.uncc.edu --------------------------------------------------------------------------- If you are not the intended recipient of this transmission or a person responsible for delivering it to the intended recipient, any disclosure, copying, distribution, or other use of any of the information in this transmission is strictly prohibited.

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Tool Integration: SOAPaligner/soap2
by Branden Timm 17 Aug '10

17 Aug '10

Hello, I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test integration case. soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder takes a FASTA files and generates a set of 13 different index files, which soap needs in order to do it's alignment. I have started by just creating the tool XML configuration for 2bwt-builder. The configuration follows: <tool id="2bwt-builder" name="2bwt-Builder"> <description>build index files for the SOAPaligner/soap2</description> <command>2bwt-builder $input</command> <inputs> <param type="data" format="fasta" name="input" label="Source file"/> </inputs> <outputs> <data format="tabular" name=".amb Index File"/> <data format="tabular" name=".ann Index File"/> <data format="tabular" name=".bwt Index File"/> <data format="tabular" name=".fmv Index File"/> <data format="tabular" name=".hot Index File"/> <data format="tabular" name=".lkt Index File"/> <data format="tabular" name=".pac Index File"/> <data format="tabular" name=".rev.bwt Index File"/> <data format="tabular" name=".rev.fmv Index File"/> <data format="tabular" name=".rev.lkt Index File"/> <data format="tabular" name=".rev.pac Index File"/> <data format="tabular" name=".sa Index File"/> <data format="tabular" name=".sai Index File"/> </outputs> </tool> I've used the tabular data type for the output files, which I'm not sure is correct. When the script runs, it generates 13 output files in my history, but they are all empty according to galaxy. When I look at galaxy_dist/database/files/.../, the output files have been generated correctly and are non-empty. Where am I going wrong? Thank you in advance for any advice. -- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm(a)glbrc.wisc.edu

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