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

add new slurm-drmaa runner to galaxy-central
by Di Pe 10 Dec '12

10 Dec '12

may be some other people would find this a useful enhancement: https://bitbucket.org/galaxy/galaxy-central/issue/778/add-new-slurm-drmaa-r…

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Auto delete dataset after workflow run?
by Praveen Raj Somarajan 03 Dec '12

03 Dec '12

Hello All, Is there a way to set "auto delete" some datafiles at the end of workflow run? I'm asking this because it is sometimes useful to delete some outputs (say intermediate files, .logs, etc), for example "auto delete" .sam file after executing sam-to-bam tool, which would free-up lot of space. This is especially useful when work with large number of samples. Look forward to any comments/suggestions. Best, Raj. ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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Can't get automatic toolshed installation to work....
by Nikhil Joshi 27 Nov '12

27 Nov '12

Hi all, We just upgraded our local galaxy to the latest version and now I am trying to get automatic tool installation to work properly. I changed the universe_wsgi.ini file to enable the toolshed xml file, I created a "shed_tools" directory one above the galaxy install, and restarted galaxy. But when I try to install a repository, I get this error as a popup: "Initializing repository installation failed". I tried this with various repositories, but I get the same error. Then when I go to "Manage installed tool shed repositories", all of the repositories I tried to install are stuck in the "Cloning" state. Finally, if I try to uninstall any of them, I get this error, with a traceback: AttributeError: 'NoneType' object has no attribute 'startswith' Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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makeblastdb wrapper
by Espin, Almudena 09 Nov '12

09 Nov '12

Hi guys, I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t support the blastdb data format, so this has to be added if a makeblastdb wrapper is to work properly. I have problems modifying the registry.py, Could anyone specify which changes have to be done? Thank you

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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
by Sascha Kastens 03 Nov '12

03 Nov '12

Hi Dev-Team, are you planning or maybe working on an update which enables the possiblilty to run workflows in batch mode with paired end data? Cheers, Sascha

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Column alignment in tabular display
by Peter Cock 30 Oct '12

30 Oct '12

Hello all, I'm curious about the logic used for column alignment when displaying tabular files (which for me was the headline feature of the last Galaxy Release - I'm very pleased to have this added at last). https://bitbucket.org/galaxy/galaxy-central/issue/553 Quoting from templates/dataset/tabular_chunked.mako function renderCell(cell_contents, index, colspan){ if (colspan !== undefined){ return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } else if (DATASET_TYPES[index] == 'str'){ /* Left align all str columns, right align the rest */ return $('<td>').addClass('stringalign').text(cell_contents);; } else{ return $('<td>').text(cell_contents); } } It seems to me that the logic should be right align all numeric columns, left align the rest. At very least, columns of type 'list' should also be left aligned. Otherwise you can easily have a situation where on clicking the "eye" you get an apparently empty dataset (unless you scroll right or down). This can easily happen with FASTA to tabular (default settings), where the descriptions have commas in them (common with annotation) thus the first column is considered to be a list (and the second column type str for the sequence). If some of the later sequences in the file have very long descriptions, right aligning the description column makes the dataset appear empty. I can provide a screen shot if it would help to explain, but here is my proposed patch. Regards, Peter -- $ hg diff templates/dataset/tabular_chunked.mako diff -r 8657ada96fca templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako Fri Jun 15 16:05:48 2012 +0100 +++ b/templates/dataset/tabular_chunked.mako Mon Jun 18 16:23:44 2012 +0100 @@ -17,8 +17,8 @@ if (colspan !== undefined){ return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } - else if (DATASET_TYPES[index] == 'str'){ - /* Left align all str columns, right align the rest */ + else if (DATASET_TYPES[index] == 'str' || DATASET_TYPES[index] == 'list'){ + /* Left align all str and list columns, right align the rest */ return $('<td>').addClass('stringalign').text(cell_contents);; } else{

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Hiding a tool via tool_conf.xml
by Peter Cock 30 Oct '12

30 Oct '12

Hi all, I'm aware that in an individual tool's XML wrapper you can add hidden="true" to the <tool> element to hide the tool from the listing shown in Galaxy's left hand panel (but the tool is still loaded and can be called by old workflows etc). Can this be done via the tool_conf.xml file as well? This would seem useful from a system configuration point of view where it seems wrong to edit the tool wrappers themselves. In fact, it might also be nice to add hidden="true" support to <section> as well as <tool> in tool_conf.xml - although I'm not so sure how useful that would be. Peter

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Re: [galaxy-dev] Using $NSLOTS in tools to control thread number
by Peter Cock 19 Oct '12

19 Oct '12

On Fri, Jun 15, 2012 at 4:38 PM, James Taylor <james(a)jamestaylor.org> wrote: > This is exactly what I think we should do (and have for a long time), but I > think the variable should be something like: > > GALAXY_CPUS > > (threads is not accurate, a multithread or multiprocess job might want to use > this info, something even more abstract than CPUS might make sense, but > SLOTS has never made sense to me). I agree that a Galaxy specific name makes a lot of sense, and that the SGE term "slots" is a bit odd. Using CPUS however is potentially ambiguous with CPUs vs cores - my desktop has two quad core CPUs, i.e. 2 CPUs but 8 cores. Where do you think this number should come from? A new entry in the runner URL is simple albeit potentially redundant with cluster-specific entries in the runner URL. As to the alternative (doing it automatically), for PBS and SGE determining the number of cores from the cluster configuration and/or parsing the cluster runner URL sounds doable - what about the other backends? Peter

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ToolShed README files, was: Blast2GO local instance
by Peter Cock 27 Sep '12

27 Sep '12

On Tue, Apr 3, 2012 at 12:16 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > > On Apr 3, 2012, at 6:07 AM, Peter Cock wrote: > >> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: >>> >>> On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: >>>> >>>> Have you seen the README file that comes with the >>>> Blast2GO wrapper? Perhaps the 'install from toolshed' >>>> could be tweaked to make this kind of documentation >>>> more visible... >>> >>> If you are installing a single repository that contains a file named one of >>> (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of >>> the file will be displayed on the "tool panel section selection page". An >>> example using the antismash repository on the main tool shed is below. This >>> new feature is available in change set revision 6945:5ea04ccb61e8, which is >>> currently running on the Galaxy tool shed and our central development >>> repository. It will be available in the next Galaxy distribution. >> >> Great. In this case I've actually called the file blast2go.txt (to match >> the use of blast2go.xml and blast2go.py). I didn't want to use a >> generic name like README since there could be other tools >> installed in the same folder (this predates the auto-install system). >> Is this naming pattern common used enough to justify including in >> the Galaxy Tool Shed code for spotting a README file? > > > Since the "read me" file contains instructions for installing the tools > in the repository, would it be better to assume only 1 installation file > that includes different instructions per contained tool if necessary? > If multiple "read me" files are allowed per repository, they would all > have to be merged together with the entire content displayed on > the tool panel section selection screen anyway, so allowing only > a single file would be better. The "read me" in your blast2go > repository is named blast2go.txt, so I suppose we could expand > the read me file name list to include <repository name>.txt. I'll do this. Hi Greg, Could you include <repository name>.txt on the list of README filenames looked for by the ToolShed as you said please? I've just checked and it isn't working at the moment. e.g. blast2go, seq_rename, clinod, venn_list, ... - in fact most of my tools :( Thanks, Peter

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FreeBayes bug - update to a toolshed tool wrapper
by Lance Parsons 11 Sep '12

11 Sep '12

I have been using the FreeBayes tool in our local Galaxy instance for some time. As FreeBayes is a rapidly evolving tool, it has been very helpful to have Daniel Blankenberg work on keeping an updated wrapper. Recently, I've run into a rather troublesome bug in FreeBayes (https://github.com/ekg/freebayes/issues/22) that is causing it to crash on nearly every real dataset. Luckily, the bug has been fixed in the latest version of FreeBayes (0.9.6_9608597d12e127c847ae03aa03440ab63992fedf). Unfortunately, the latest version has a few parameter changes that require an update to the wrapper code. I've taken the liberty to make some changes to the wrapper and they seem to work. However, now that I have the tool installed from the Tool Shed, I'm not sure of the best way to 1) incorporate this update into my local galaxy instance and 2) contribute this change back to the Tool Shed. The best solution is to get the Tool Shed updated and then pull that update into my production Galaxy instance, however, I'm wondering if there is a way I could push "hot-fixes" to my production instance without causing me headaches down the line when the Tool Shed is inevitably updated. As far as coordinating updates of Tool Shed tools, I suppose the process might be different for different tool authors. I was wondering, however, if anyone had thoughts on how this might work best. I've created a clone of the galaxy tool shed repository in Bitbucket (https://bitbucket.org/lance_parsons/freebayes/) and given Daniel and Greg access to it in hopes that would make things easier.Let me know if there is a better way to coordinate, etc. Thanks again. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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