- galaxy-dev - lists.galaxyproject.org

Some questions about histories
by Sascha Kastens 16 Aug '12

16 Aug '12

Hi all! I have two questions about histories in Galaxy: 1. Is it possible to mark/set a history as published via the API? 2. How can I get the ID of the current users history via a tool? Something like ${__app__.model.User.get($__user_id__).histories[0].id} ?! Thanks in advance! Cheers, Sascha

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Re: [galaxy-dev] Conditionally showing certain form elements on tool page
by Dan Tenenbaum 15 Aug '12

15 Aug '12

Hi John, On Wed, Aug 15, 2012 at 7:32 PM, John Patterson <jmpatt4(a)g.uky.edu> wrote: > On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: > > Hi all, > > I'm trying to wrap my head around what the <conditional> tag does...it > looks like it doesn't do what I would like. > > I want to create a tool that allows the user to upload a data file and > then have it run through one or more filters. Each filter takes one or > more parameters. > > I was thinking I could do something like this: > > > <inputs> > <conditional name="mycond"> > <param name="checktest" type="boolean" label="foo" value="yessir"> > </param> > <when value="yessir"> > <param name="param1" type="text" label="bar" value="twunk"> > </param> > </when> > </conditional> > </inputs> > > The idea being, if the user checks the box labeled "foo", a text box > labeled "bar" will appear. > And I would have several such checkboxes and their accompanying parameters. > But what I get is just the checkbox, and nothing happens when I click it. > > Is it possible to do what I have in mind, and if so, how? > > Also note that these conditions are not mutually exclusive. A user can > select one *or more* filters. So I'm not sure how the body of my > <command> tag should look. Is there a way I can just pass every > possible parameter to my script like this: > myscript.py param1=foo param2=bar > If a parameter is not defined (because the user didn't click its > associated checkbox), then the script will receive e.g. > param1= param2=bar > but it can deal with that. > > I realize I can make several tools and chain them together in a > workflow, but that seems like overkill for this use case, and it would > be nice if the user could set up their desired filters on one screen. > > Is this possible? > Thanks! > Dan > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > Hello Dan, > > This page really helped me understand how the tags worked as well as looking > at some older tools: > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Thanks for the pointer. I have seen this page, but I'm still stuck. I'll read it again more carefully though. > > I will take a look at my tool when I get to the office tomorrow. Thanks. I appreciate it! Dan > > John > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/

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Another trackster issue?
by SHAUN WEBB 15 Aug '12

15 Aug '12

I am looking at bigwig files in trackster. When I zoom in the point where 20kb is displayed on screen I get large blocks of the track separated by empty gaps. When I zoom in to these gaps there is definitely track signal there. Is this a bug or is this intended to limit the amount of data to load? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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refresh user history
by Quang Trinh 15 Aug '12

15 Aug '12

Hi dev, We have a script that download a number of files from an external site, however, only the first file shows up in the user history once the downloads are complete. The rest of the files show up when we click on the refresh user history button. Is there a way to refresh the user history in our script when all the files are downloaded? THanks, Q

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File upload via ftp: FileZilla
by suzan katie 15 Aug '12

15 Aug '12

Hello everyone, I am trying to upload files (size:6GB) via ftp and i am using FileZilla for ftp upload of files. Host/usernames and password details as follows: Host: main.g2.bx.psu.edu Username: My galaxy Username Password: Galaxy password I found this tutorial for FTP upload. http://screencast.g2.bx.psu.edu/quickie_17_ftp_upload/flow.html I am getting an error message: Could not connect to server Status: Connection attempt failed with "ECONNREFUSED - Connection refused by server". Is there any other method followed for ftp file upload? Any help or advice is appreciated Thanks Suzan

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Upload File: how to see all registered formats ?
by Marc Logghe 15 Aug '12

15 Aug '12

Hi again, Emboss_datatypes is installad via tool shed. The 'View datatypes registry' in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank. However, the 'Upload File' tool does not show genbank in the 'File Format' dropdown. How can one configure the upload1 tool so that all registered formats are listed ? I don't understand the from_parameter hocus-pocus in this line (upload.xml): <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ? Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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problems in integrating tools to GALAXY
by Jenny 15 Aug '12

15 Aug '12

Hi, Dear all, I am trying to integrate a perl script to GALAXY, and here are the problems. I have a tool configuration xml file called abc.xml located at tools/myTools directory, which calls a perl scripts called toolExample.pl. 1 <tool id="abc" name="abc"> 2 <command interpreter="perl">toolExample.pl $input $output</command> 3 <inputs> 4....... 5...... Inside the toolExample.pl, I am using some linux system command such as "wc" and also "BEDTools/windowBed". The BEDTools executables are configured correctly in my local linux machine, and when I type "which windowBed" it can give me back the path correctly. When I run toolExample.pl outside galaxy in the terminal, everything looks correct; but when I run galaxy, it gave me the nonsense results ( all 0) and it seems that GALAXY has problems in recognizing either the windowBed excutable file or the linux system command "wc" or maybe both. To let GALAXY recognize "windowBed", I tried to put the windowBed executable copied to myTools directory and add the following <requirements>tags to the abc.xml file, but it doesn't seem to be working. ..... <requirements> <requirement type="binary">windowBed</requirement> </requirements> .... Could anyone please help me figure out what was wrong? How can I fix the problem? Thank you very much in advance! Best, Jenny

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how to edit attributes of tool
by Robert Chase 14 Aug '12

14 Aug '12

Hello, Is there a way to annotate the notes of a custom tool to include information about the parameters passed to the tool? Let us say a user specifies a number n as a parameter to the tool. Is it possible to put this parameter in the notes that appear when the pencil icon is pressed? Reading the notes under the <data> tag set, wiki.g2.bx.psu.edu/Admin/Tools/Tool Config Syntax I didn't see any hint about how to pass the script parameters to the metadata boxes under the pencil icon. -Rob

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Local Galaxy concept system: hardware spec questions
by Sebastian Schaaf 14 Aug '12

14 Aug '12

Hi all, I have a couple of question around the topic "hardware requirements" for a server which is intended to be bought and used as concept machine for NGS-related jobs. It should be used for development of tools and workflows (using Galaxy, sure) as well as platform for some "alpha" users, who should learn to work on NGS data, which they just began to generate. This concept phase is planned to last 1-2 years. During this time main memory and especially storage could be extended, the latter on a per-project basis. We will start with a small team of 3 people for supporting and developing Galaxy and system due to the user's requirements, and the first group of users will bring in data, scientific questions and hands-on work on their own data. Main task (regarding system load) will be sequence alignment (BLAST, mapping tools like BWA/Bowtie), and after that maybe some experimental sequence clustering/de novo assembly for exome data. Additionally variant detection in whatever form are targeted. Only active projects will be stored locally, data no more in use will be stored elsewhere in the network. So far for the setting, regarding the specs the following is intended: - dual-CPU mainboard - 256 GB RAM - 20-30 TB HDD @ RAID6 (data) - SSDs @ RAID5 (system, tmp) Due to funding limitations it may be the case that RAM has to be decreased to 128 GB, not solved is currently the question, if it will be enough for those SSD bundle in RAID5, maybe we have to go for only two of them in RAID1. What we try to find out is, where in those described tasks the machine would run into bottlenecks. What's pretty clear is that I/O is everything, already by a theoretical point of view. But we also observed that on a comparable machine (2x 3,33 Ghz Intel 6-core, 100GB RAM, 450 MB/s R/W to data RAID6). The question of questions is right at the beginning of configuring a system, if one should go for an AMD or an Intel architecture system. The first offers more cores (8-12) at a lower frequency (~2,4 Ghz), the latter less cores (6) with higher frequency (~3,3 Ghz). Due to the data sheets, the Intel CPUs are on a per-core basis ~30% faster with integer operations and ~50% faster with floating point. The risk we see with the AMDs is on the one hand that the number of cores per socket could saturate the memory controller, and on the other hand those jobs, which can not or only poorly be parallelized need more time. To bring all this to some distinct questions (don't feel forced to answer all of them): 1. Using the described bioinformatics software: where are the potential system bottlenecks? (connections between CPUs, RAM, HDDs) 2. What is the expected relation of integer-based and floating point based calculations, which will be loading the CPU cores? 3. Regarding the architectural differences (strengths, weaknesses): Would an AMD- or an Intel-System be more suitable? 4. How much I/O (read and write) can be expected at the memory controllers? Which tasks are most I/O intensive (regarding RAM and/or HDDs)? 5. Roughly separated in mapping and clustering jobs: which amounts of main memory can be expected to be required by a single job (given e.g. Illumina exome data, 50x coverage)? As far as I know mapping should be around 4 GB, clustering much more (may reach high double digits). 6. HDD access (R/W) is mainly in bigger blocks instead of masses of short operations - correct? All those questions are a bit rough and improved (yes, it IS a bit of a chaos currently - sorry for that), but any clue to a single question would help. "Unfortunately" we got the money to place the order for our own hardware unexpectedly quick, and we are now forced to act. We want to make as few cardinal errors as possible... Thanks a lot in advance, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Chair of Biometry and Bioinformatics Department of Medical Information Sciences, Biometry and Epidemiology University of Munich

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Re: [galaxy-dev] Local Galaxy concept system: hardware spec
by Paul-Michael Agapow 14 Aug '12

14 Aug '12

Some quick answers in the hopes that more qualified people will chip in: I have a couple of question around the topic "hardware requirements" for a server which is intended to be bought and used as concept machine for NGS-related jobs. First a comment - it sounds a bit like you are where we were 12 months ago in developing our Galaxy system and looking at similar needs. I think you'll almost always need more of everything, because people will always be analysing bigger datasets, building bigger assemblies, etc. 1. Using the described bioinformatics software: where are the potential system bottlenecks? (connections between CPUs, RAM, HDDs) While I/O is potentially a bottleneck (due to Galaxy copying and writing the datasets etc.), I wonder if in practice this is the case. Many of the NGS tasks are so long running that I/O issues may not be a significant hit. However, you may have a potential bottleneck in getting data onto the system. How does information get from the sequencer into the Galaxy instance? This may need some thinking about. 2. What is the expected relation of integer-based and floating point based calculations, which will be loading the CPU cores? I have no idea what this means. 3. Regarding the architectural differences (strengths, weaknesses): Would an AMD- or an Intel-System be more suitable? I don't think this will make any difference. If it's a question of the number of cores, that depends to some extent on how many concurrent users or tasks you'll have running. I suspect your number of concurrent users will be low (i.e. at any time, very few people and logged in and running stuff under Galaxy). 6. HDD access (R/W) is mainly in bigger blocks instead of masses of short operations - correct? That's my impression. ------ Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency (UK) ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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