August 2011 - galaxy-dev - lists.galaxyproject.org

Request for pulling the updated FASTQ (de-)interlacer tool
by Florent Angly 05 Aug '11

05 Aug '11

Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository: https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent

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BWA wrapper with Illumina-1.3+ FASTQ files
by Assaf Gordon 05 Aug '11

05 Aug '11

Hi, The attached patch enables the BWA wrapper to work with Illumina-1.3+ FASTQ files without Grooming (which goes well with the name of the tool: "Map with BWA for Illumina" ). Actually, Changing the XML and the python code, testing the tool and mapping to the mouse genome all together took less time than grooming one 4.2GB FASTQ file :) Comments are welcomed, -gordon

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Optional column select arguments?
by Peter Cock 05 Aug '11

05 Aug '11

Dear all, I'm trying to define an *optional* column parameter as follows: <param name="start_col" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" optional="True" label="Column containing start co-ordindate" help="Leave empty to include everything from the first base/residue"/> i.e. I want the user to either select ONE of the columns of the input tabular data file (in which case getting "1" or "c1" etc as the string is fine) OR pick no column at all (in which case I want an empty string or similar in the command string. Is this possible? The above parameter loads fine, but defaults to the first column with no apparent way to un-make this implicit selection. Thanks, Peter

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Re: [galaxy-dev] [galaxy-user] galaxy cluster setup
by Jennifer Jackson 05 Aug '11

05 Aug '11

Hello Bernard, I am going to cross-post your email over to the galaxy-dev mailing list, where there are many users doing these same sort of configuration tasks. Perhaps some of them have will also have comments and advice. Best! Jen Galaxy team On 8/5/11 6:15 AM, Bernhard Gschloessl wrote: > Dear all, > > I wonder if someone of you has already tested Galaxy with the ProActive > scheduler (since it is not listed on the page > http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster )? If yes, > could you give me a feedback? > > Thanks in advance, > Bernhard >> >> >> >> From: *Roman Valls* <brainstorm(a)nopcode.org >> <mailto:brainstorm@nopcode.org>> >> Date: Thu, Jun 16, 2011 at 4:41 PM >> Subject: Re: [galaxy-user] galaxy cluster setup >> To: galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> >> >> >> Hello Robert, >> >> You may have a look at the official documentation on the wiki: >> >> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster >> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer >> >> You may also have a look at the slides from the past Galaxy Community >> conference: >> >> http://wiki.g2.bx.psu.edu/GCC2011 >> >> You might be interested on the one Nate Coraor gave: >> >> "Galaxy Deployment and API" >> >> Cheers ! >> Roman >> >> On 2011-06-15 23:01, Robert Jackson wrote: >> > Does anyone have practical info on galaxy setup on a cluster? -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Problem with Tool Shed mock ups?
by Peter Cock 04 Aug '11

04 Aug '11

Hi Greg, I think I've found a problem on the tool shed mockups - in the case of Konrad's interproscan (username konradpaszkiewicz) there seem to be error messages rendered, e.g. System Message: WARNING/2 (<string>, line 2); backlink Inline strong start-string without end-string. ... System Message: ERROR/3 (<string>, line 17) Can you reproduce this? Should I file a bug? Looking at Konrad's XML file, perhaps the tool doesn't like the space in the first help line? (star)(star)Interproscan(space)(star)(star) I've not installed the XML file locally to see how it is rendered within Galaxy. Peter

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cufflinks 1.0.3
by Glen Beane 04 Aug '11

04 Aug '11

just wondering if anyone else in Galaxy land was having this problem, I emailed tophat.cufflinks@ to let them know We have been experiencing segmentation faults with cufflinks 1.0.3. Our platform is CentOS 5.5, and we compiled from source using gcc 4.1.2 (Red Hat 4.1.2-48). The segmentation fault occured when we passed in a GTF annotation file with the -G option. Using gdb, I tracked it down to line 218 in bundles.cpp: string rs = (rna_seq) ? rna_seq:""; It appeared that in our case rna_seq was uninitialized and did not point to a valid C string. char* rna_seq; if (loadSeqs && faseq) { rna_seq = rna.getSpliced(faseq, false, &seqlen); } ... if (loadSeqs) { string rs = (rna_seq) ? rna_seq:""; ... } As you can see, it would be possible for the first if-block to not execute, but the second one to still execute (loadSeqs = true, faseq = false). I tried making the following change to the declaration of rna_seq to initialize it to NULL: char* rna_seq = 0; this stopped the segmentation fault we were seeing -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153

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Re: [galaxy-dev] [galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install)
by Peter Cock 03 Aug '11

03 Aug '11

Note: Local install questions are normally directed to the galaxy-dev list (CC'd) rather than galaxy-user On Mon, Aug 1, 2011 at 3:21 PM, Joseph Hargitai <joseph.hargitai(a)einstein.yu.edu> wrote: > Enis, > > a few things we came across: > > a, local install > > R - not the correct download url, Which URL are you talking about? The wiki page on dependencies http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies correctly links to the R project as http://www.r-project.org/ > rpy - will this be fixed? What needs to be fixed? Moving Galaxy to rpy2? https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest… > permissions: > > the script seems to use sudo and galaxy interchangeably, which creates an > issue with permissions writing to folders. > > Is there a way to install as galaxy user only? Do you mean installing Galaxy without admin rights (i.e. without using sudo)? > If we do need the switching between sudo and galaxy - is there a set of > directory permissions you suggest for the original galaxy-dist install and > the galaxyToools folder? Good question - having manually reset permissions on a test server while debugging driving mappings, I'd like to know what they should be. Are you planing on using the Linux user group functionality as part of your setup? e.g. Both your personal account and the Galaxy user account could be part of a Galaxy admin group. > b, > as a second category of questions: > are there any tools that do not work on the standard cloud install? (skipped > over entirely or installed but do not work?) By that do you mean of the standard tool set in the main repository? (Because there will be lots of Galaxy tools in the Tool Shed which are not in the standard cloud install). Peter

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scripts/make_egg_packager.py broken
by Sonderegger Bernhard 03 Aug '11

03 Aug '11

Hi all, The scripts/make_egg_packager.py script appears to be broken I get the following message: Traceback (most recent call last): File "scripts/make_egg_packager.py", line 21, in <module> c = Crate() TypeError: __init__() takes at least 2 arguments (1 given) Thanks for any suggestions. B.

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Creating and adding new repositories for the new tool shed
by Nikhil Joshi 03 Aug '11

03 Aug '11

Hi all, I have been using Galaxy for a few years now and I am about to start creating my own repositories for the new Tool Shed. However, I can't seem to find any good documentation on how to do that exactly. Can someone point me in the right direction? I need to figure out the best way to organize a repository, the XML format for the XML file, and any other important things that I might need to know? Is there a good resource for all that? The wiki has a section entitled "Create a new repository", but there is nothing in it. Any help would highly appreciated. Thanks! - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.edu

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Hidden history item
by Bossers, Alex 03 Aug '11

03 Aug '11

Hi all, by default I let my tools produce ("the old way") a logfile of the console and additional running statistics. This is convenient at tool setup and ocassionally for troubleshooting. Anyway I would like to make the corresponding history item hidden. I tried including hidden="true" in the output tag but that does not make any difference. Is this possible at all or only applicable to running workflows? Any pointers appreciated. Alex

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