- galaxy-dev - lists.galaxyproject.org

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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Workflow Bug?
by John Chilton 02 Aug '11

02 Aug '11

Hello Galaxy Developers, I have a user who noticed a potential bug when extracting workflows from histories on our local Galaxy server. I have recreated the bug on the public Galaxy server with a much smaller history. The history can be found here: http://main.g2.bx.psu.edu/u/jmchilton/h/column-join-workflow-bug Basically when creating workflows from such histories, the second input to "Column Join" never seems to be connected to the previous step the way I would expect it to be. In the workflow editor you can manually create this connection, but it is easy to miss this in a large worfklow and have incomplete results as a consequence. Am I missing something or is this a bug? Thanks for your time, -John

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Question on timing with API, running workflows, and setting metadata
by Duddy, John 02 Aug '11

02 Aug '11

I'd like to have an external program that registers a file by absolute path (link, not upload) in a data library, then immediately starts a workflow on it. My question is to whether or not that will work in the general case where: - The system is configured to set metadata externally - The compute grid is busy (so the set_meta call is queued for some time) In this case, will the workflow be queued and set idle, waiting for the set_meta() to complete? Or will the API call to register the data library block until the set_meta() is done? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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Does Galaxy have a tool to run R script?
by liu bo 02 Aug '11

02 Aug '11

Dear all, I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help. Thank you, Bo Liu

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Nucleolar localization sequence Detector (NoD)
by Peter Cock 02 Aug '11

02 Aug '11

Dear all, I've just uploaded my Galaxy wrapper for command line NoD (clinod) to the Galaxy tool shed (under the Sequence Analysis category): http://usegalaxy.org/community NoD is from the Barton group at the University of Dundee, and does Nucleolar localization sequence (NoLS) prediction. There is also a web version: http://www.compbio.dundee.ac.uk/www-nod/ I promised this during my Galaxy Community Conference talk earlier in the year, and now that clinod v1.3 has been formally released I'm delighted to share this wrapper as well. My thanks to Peter Troshin and the rest of the NoD team for their help. Regards, Peter

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