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

18 Aug '10

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

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megablast options in galaxy
by Ameena Nalim 17 Aug '10

17 Aug '10

Hi! Can any one tell me how to select against the human and mouse databases when running megablast in galaxy? When I run my dataset directly in NCBI Blast I get more realistic hits for my algal samples. There is no way I can have mouse or rat in my metagenomic samples of algal cultures. Alternately, can I import BLAST output files into galaxy? thanks Ameena Nalim

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Static content fails to render
by Andrew Stewart 17 Aug '10

17 Aug '10

Just installed galaxy, but the static content is failing to render and I'm not sure why. Screenshot of browser: http://i38.tinypic.com/34rgjlv.png My httpd.conf contains the following: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/src/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/src/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/src/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/src/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/src/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

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question about fastq groomer
by kenlee nakasugi 17 Aug '10

17 Aug '10

Hi All, I'm new to NGS analysis, and command line analysis for that matter. (I'm in the process of learning perl/python - so please bear with this newbie query). I've installed the fastx-toolkit and the scripts here are working great, but couldn't find the fastq_groomer script anywhere on the galaxy page, at http://hannonlab.cshl.edu/fastx_toolkit/index.html, nor on the web, except from this page: http://bitbucket.org/galaxy/galaxy-dist/src/tip/tools/fastq/ I tried running it via: python fastq_groomer.py input_file input_type output_type as per the fastq_groomer.xml, but doesn't work. Is this the correct fastq_groomer script, am I running it correctly, or where can I get this script to run like the other fastx-toolkit scripts? I know I could use the Galaxy server/ or install galaxy locally, but for several reasons at the moment want to use the individual scripts. Thanks in advance! Ken Kenlee Nakasugi School of Molecular Bioscience University of Sydney

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galaxy and mobyle xml wrappers
by alex 12 Aug '10

12 Aug '10

Is there a software that will convert my Mobyle xml wrappers to Galaxy xml wrappers? Alex

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Embedabble workflows and automating execution
by Alex Quezada 12 Aug '10

12 Aug '10

Two questions: 1. Is it possible to embed a workflow inside another workflow? 2. Is it possible to run a workflow via command line so that the execution could be automated? Say some other process produces the inputs, then command line or some other API (url maybe?) passes a reference to the inputs and kicks off the workflow. I found this, but no resolution: http://bitbucket.org/galaxy/galaxy-central/issue/43/workflow-command-line-e… ************************************************ Alex Quezada Software Developer Genome Science/Joint Genome Institute (B-6) Bioscience Division MS M888 Los Alamos National Laboratory Los Alamos, NM 87545 phone: (505) 606-2153 fax: (505) 665-3024 email: alexq(a)lanl.gov ************************************************

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Non-admin users uploading from paths
by Adam Labadorf 11 Aug '10

11 Aug '10

Hello, I'm trying to configure a non-admin user to upload data to our local galaxy instance. We manage our NGS data separately from galaxy and add access to them using the Import from system paths functionality. The non-admin user I have configured can upload from a local file or import from history but does not have the menu item to add files from systems paths like my admin user does. Is there a way to enable non-admin users to add datasets from system paths? -- Adam Labadorf Computational Tech Fraenkel Lab, MIT labadorf(a)mit.edu

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downloading screencasts?
by Erick Antezana 09 Aug '10

09 Aug '10

Hi, I remember that some time ago I was able to download some screencasts (as MOV files). Is it still possible to grab them from somewhere in the Galaxy wiki? if so, from which location? cheers, Erick

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display a bed with track definition line
by Davide Cittaro 07 Aug '10

07 Aug '10

Hi there, is there a way to display a bed file to UCSC setting the track name and description automatically? I mean, if the bed file contains only the data tabular data, how can I add "track type=bed name=dataset.name" at display time? I get a generic "User track" instead, that means that I have to rename it every time in the UCSC browser (otherwise it will be overwritten by any other custom track ) d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Mapping Unmapped sequences to other guessed contaminants
by Antony Jose 07 Aug '10

07 Aug '10

Hi, I am a relatively new user to Galaxy. Of the 21 million mappable illumina reads, 17 million mapped to a reference genome. I would like to know if the remaining 4 million come from a known contaminating sequence for which I have a .txt file. Is there an easy way of doing this in Galaxy? Please advice. Thank you. Antony

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