May 2013 - galaxy-dev - lists.galaxyproject.org

Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset
by Jean-Francois Payotte 07 May '13

07 May '13

Dear Galaxy mailing-list, We are currently facing a strange issue with our local Galaxy installation (distribution from Jan. 11 2013). I'm going to try to describe the problem as much as I can, and feel free to ask for more details if it can help in solving this issue. So basically, we have a situation where (about half the time), when a job ends in error, the error message (shown when clicking on the bug icon), doesn't seem to be related to the dataset in error. As this particular problem seem to be present only when datasets ends in error, I created a simple python script which simply does 2 things: It outputs the hostname to stdout (in order to investigate if the problem is node-dependant) It outputs the following message "This is an error message printed to stderr", to stderr. (This is done in order to get only error datasets and to investigate the before-mentioned issue.) Here is the code of my python script: import sys import socket def main(): print socket.gethostname() sys.stderr.write('This is an error message printed to stderr\n') if __name__ == '__main__': main() I ran this tool about 50 times and I looked at the error messages displayed both in the preview section of the dataset (in the history), and the error message displayed when clicking on the bug icon "view or report this error". About half the time, the results were as expected: the dataset stdout would read the name of the node where the job was executed the dataset stderr would read: "This is an error message printed to stderr" and the error message displayed when clicking on the bug icon would be: Dataset generation errors Dataset 54: Test error Tool execution generated the following error message: This is an error message printed to stderr The tool produced the following additional output: some.server.name However, the other half of the time, the error message shown in stderr doesn't correspond to the error message displayed when clicking on the bug icon: the dataset stdout is still reading the name of the node the dataset stderr is still reading "This is an error message printed to stderr" but the error message displayed when clicking on the bug icon would be something like: Dataset generation errors Dataset 3: chrM.bed Tool execution did not generate any error messages. We can clearly see a discrepancy between the error message in stderr and the error message of the bug report. Actually, the bug report is saying that there is not any error and it makes reference to some "Dataset 3: chrM.bed", even when the actual dataset is "Dataset 53: Test error". There is absolutely no .bed file in my history and the dataset 3 actually reads "Dataset 3: Test error". Some of the datasets mentioned in the faulty bug reports seems to be really old datasets (like one year old). So my question to you is, could this be related to some mix-up between datasets ID? And how can I look this up. I must say that at the moment, I have absolutely no idea how to solve this issue. Many thanks for your help! Best regards, Jean-François

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conditions within workflows
by Olivia Doppelt 07 May '13

07 May '13

Dear developpers, I have a question concerning the insertion of conditions inside workflows ? Here, at the pasteur Institute, we would like to use galaxy to create a microbiome analysis workflow. However, it requires at least 10 different tools which may be or may not be used in several cases. For the moment, all I see is to create a giant wrapper for this workflow but it would be loosing the great interest of galaxy. I see on bitbucket that there is a branch on galaxy-central named "galaxy-central-conditional-toolbox-elements" are there new elements since february ? Best regards, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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tool shed installations and grouping in categories
by Björn Grüning 07 May '13

07 May '13

Hello all, during the last weeks the tool shed team did a lot of awesome work and soon it should be possible to install meta-packages like Ira's proteomics pipeline or the ChemicalToolBoX with a few clicks. Installing all nested dependencies, datatypes and so on automatically. One last problem I'm seeing is the grouping of tools in categories. If you install all your tools via a meta package you don't have any choice to group single tools in single categories. The same problem applies when your repo have more than one tool that do not fit in one single category. Before we had the repository dependencies features in Galaxy I shipped example tool_conf.xml files and explained how to modify it manually. These example files contained the tool-path with tools ID and the categories with ID. What do you think about shipping such files in a repository and during installation you offer a third choice to the user (next to, choose category, enter new category name) ... something like "accept included suggestions" and display them. Also for the installation via the API it would make installing a completely new Galaxy flavour easy. Any comments or ideas? Cheers, Björn

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List of genomes
by Lee Katz 06 May '13

06 May '13

Hi, I am wondering what I can do to add more genomes to this list (hopefully this image will make it through the mailing list). I am importing fastq files from a MiSeq run. We are using a modified version of Galaxy called Tron. Everything I see on the wiki is about adding custom reference genome assemblies, but I don't understand what to do about adding a species without the reference assembly. Without the correct species, I am forced to use the option "unspecified (?)" Thanks for your help. [image: Inline image 3] -- Lee Katz, Ph.D.

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Improving the change revision view on the Tool Shed
by Peter Cock 06 May '13

06 May '13

Hello all, I've noticed a couple of weaknesses in the current revision view for the Tool Shed. First, the commit comment is not shown - this would make sense next to the revision number and above the diffs. Second, there is no easy way to jump to the next/prev revision, you must first go back to the "View change log" page. Perhaps simple prev/next links would work well, or as used elsewhere in the Tool Shed a revision drop down control [*]? Regards, Peter [*] Use with caution, I've found this focus issue quite infuriating: https://trello.com/card/-/506338ce32ae458f6d15e4b3/821

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user password different type encoding
by Vipin TS 06 May '13

06 May '13

Hello dev-team, I would like to add the different type of password encryption to the users in my galaxy instance. I started working with the current password encoding script: /home/apps/galaxy-dist/lib/galaxy/util/hash_util.py I will keep the current sha1 and add another layer of encryption to the sha1 hash, otherwise I need to force all my users to change the password and follow the new hashing method. Can anyone please point me any other place/script which I missed regarding the encryption/decryption of user authentication. thanks in advance, --/Vipin

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Usability bug/inconsistency with workflows versus tools
by Peter Cock 06 May '13

06 May '13

I seem to be in feedback mode: another little rough edge in Galaxy: When using a tool in Galaxy, at the end of the parameters there is a nice eye catching blue button labelled "execute". When running a workflow in Galaxy, the equivalent button is plain grey and reads "Run workflow". I think it would be clearer if this was the same blue style, and perhaps also labelled "execute". Regards, Peter

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Re: [galaxy-dev] Running Galaxy through Apache
by Jeffrey Long 06 May '13

06 May '13

1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website? Those are the only ones I changed. I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me. Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly. Exception happened during processing of request from ('127.0.0.1', 47424) Traceback (most recent call last): File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__ self.handle() File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__ return self.app(environ, start_response) File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__ path_info = self.normalize_url(path_info, False)[1] File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url AssertionError: URL fragments must start with / or http:// (you gave '.') 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time? I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour. Thanks, I'll try to remember to 'reply-all' here! -Jeff On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <aebrenne(a)uci.edu> wrote: > Hia Jeff, > > I think this is related to the proxy settings in Galaxy (universe_wsgi.ini) > > What is happening is that if you look at the source code for your > galaxy website, it is trying to load css/images from: > http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if > you visit that link it offers you a 404 not found. Make sure the proxy > settings in your universe_wsgi.ini is set correctly. > > If it is, it could be that you need to setup proxies for the > subdirectories as well. If you look at the nginx guide here: > http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy > you will notice that we provide alias for /static/*. > > In terms of doing this in Apache, you may need to add more proxy pass > lines that correspond to the subdirectories in question. > > > Be sure to post back to the Galaxy listsrv so that future people may > benefit from this! > -Adam > > -- > Adam Brenner > Computer Science, Undergraduate Student > Donald Bren School of Information and Computer Sciences > > Research Computing Support > Office of Information Technology > http://www.oit.uci.edu/rcs/ > > University of California, Irvine > www.ics.uci.edu/~aebrenne/ > aebrenne(a)uci.edu > > > On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <jlong1(a)ualberta.ca> wrote: > > Hi Adam thanks for the response, > > I'm not using VirtualHosts. I just copied the lines shown into > > /etc/apache2/apache.conf (this is on Ubuntu Linux). > > > > I copied the lines you list (with appropriate modification) into this > same > > apache.conf. That seems to work - as far as Apache goes! However, when > I > > load galaxy in a browser now, I get a bunch of gobbledigook (it looks > like > > the frames aren't being built properly or something). You can take a > look; > > I've temporarily enabled the site to be world-viewable. > > > > http://trove.usask.ca/galaxy > > > > Thanks for your help! > > > > -Jeff > > > > > > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <aebrenne(a)uci.edu> wrote: > >> > >> Jeff, > >> > >> How / Where did you add the apache changes? Are you using VirutalHosts > >> or ... ? Quick glance, everything appears correct. Its been a while > >> since I used Apache (switched everything to nginx) however I believe > >> if you want to setup a Reverse Proxy, you need to add / use the proxy > >> pass lines which does not appear in the Galaxy Wiki. > >> > >> Something like this should work: (untested...) > >> > >> <IfModule mod_proxy.c> > >> ProxyRequests Off > >> <Proxy *> > >> AddDefaultCharset off > >> Order Deny,Allow > >> Deny from all > >> Allow from *.ualberta.ca # Change / Remove as needed > >> </Proxy> > >> > >> ProxyPass /galaxy http://localhost:8080/ > >> ProxyPassReverse /galaxy http://localhost:8080/ > >> # Line below is optional > >> Redirect permanent /galaxy http://mymachine.com/galaxy > >> > >> ProxyVia On > >> </IfModule> > >> > >> > >> Let us know, > >> -Adam > >> > >> -- > >> Adam Brenner > >> Computer Science, Undergraduate Student > >> Donald Bren School of Information and Computer Sciences > >> > >> Research Computing Support > >> Office of Information Technology > >> http://www.oit.uci.edu/rcs/ > >> > >> University of California, Irvine > >> www.ics.uci.edu/~aebrenne/ > >> aebrenne(a)uci.edu > >> > >> > >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <jlong1(a)ualberta.ca> > wrote: > >> > Hi folks, > >> > I am wanting to run a galaxy instance and serve it at a location other > >> > than > >> > the webserver root, i.e. at http://mymachine.com/galaxy rather than > >> > just at > >> > http://mymachine. > >> > > >> > To do this, I've followed the instructions about proxying Galaxy > through > >> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy. > >> > I'm > >> > pretty sure I've followed the instructions exactly. I enabled the > >> > necessary > >> > apache proxy modules and then I added these lines to my apache.conf > >> > file: > >> > > >> > > >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule > >> > ^/galaxy/static/style/(.*) > >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule > >> > ^/galaxy/static/scripts/(.*) > >> > /myplace/galaxy-dist/static/scripts/packed/$1 > >> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 > [L] > >> > RewriteRule ^/galaxy/favicon.ico > /myplace/galaxy-dist/static/favicon.ico > >> > [L] > >> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt > >> > [L] > >> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] > >> > > >> > ...and re-started the apache server without a problem (note: I also > >> > tried it > >> > commenting out everything but the first, second and last line in case > >> > there > >> > was an issue with the static stuff). > >> > > >> > I then made sure the following lines were present and uncommented in > my > >> > universe_wsgi.ini file > >> > > >> > [filter:proxy-prefix] > >> > use = egg:PasteDeploy#prefix > >> > prefix = /galaxy > >> > > >> > [app:main] > >> > > >> > filter-with = proxy-prefix > >> > cookie_path = /galaxy > >> > > >> > > >> > I start up Galaxy. And still, I can only reach it on > >> > http://mymachine:8080, > >> > not at http://mymachine/galaxy as I intend. > >> > > >> > Any help would be appreciated! Thanks! > >> > > >> > -Jeff > >> > > >> > > >> > ___________________________________________________________ > >> > 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/ > >> > > >> > To search Galaxy mailing lists use the unified search at: > >> > http://galaxyproject.org/search/mailinglists/ > >> > > > >

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"Published Workflows" missing from "All Workflows"
by Peter Cock 06 May '13

06 May '13

Hello all, This is to report a usability bug with workflows - specifically the curiously separate handling of "Published Workflows" in the user interface. 1. Log into your Galaxy account, 2. On the top ribbon, click on "Shared Data", "Published Workflows", and make a note of the entries. 3. Return to the main screen via the top ribbon entry "Analyse Data" 4. On the bottom of the left hand tool column, under "Workflows" click on "All workflows". Observe results. 5. On the top ribbon, click on "Workflows". Observe results. Actual result (in 4 and 5): Two sections, "Your workflows" and "Workflows shared with you by others" Expected result (in 4 and 5): Three sections, "Your workflows", "Workflows shared with you by others", "Published Workflows". i.e. "Published Workflows" are hidden or separated away from the others. This appears to be a design choice (like shared datasets they must be "imported" before use), but if so this could be clarified as follows: Suggested result (in 4 and 5): Two sections, "Your workflows" and "Workflows shared with you by others", plus a footnote (with link) saying something about additional workflows are available to import from "Published Workflows". Regards, Peter

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Taxonomy fetching not working
by Deepthi Thomas Kannanayakal 06 May '13

06 May '13

Hi Galaxy team, I am having problems with taxonomy information fetching.(Metagenomic Analysses->Fetch taxonomic representation). According to the following link http://dev.list.galaxyproject.org/quot-Fetch-taxonomic-representation-quot-… I have installed libraries from https://bitbucket.org/natefoo/taxonomy I have installed them in my local directory(not in /usr/local). But I am still having problem /bin/sh: taxBuilder: command not found What am I missing here? Thanks, Deeps *Deepthi Theresa Thomas Kannanayakal Bioinformatics Database Specialist Sun Visual Genomic Centre, Suite 1150, Health Science Centre 3330 Hospital Drive NW Department of Biochemistry and Molecular Biology Faculty of Medicine, University of Calgary T2N 4N1 Calgary, Alberta, Canada** * *Ph: (403) - 210 6661 Fax: (403) - 210 9538*

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