Re: [galaxy-dev] Proposed patch to blastxml_to_tabular.py

On Wednesday, November 30, 2011, Peter van Heusden wrote: > Hi there. When trying to convert some BLAST XML to tabular format, from > an old version of BLAST (2.2.15), I had to make some changes to > blastxml_to_tabular.py to get correct results. A patch is enclosed in > this message (and attached

Re: [galaxy-dev] Proposed patch to blastxml_to_tabular.py

On Wed, Nov 30, 2011 at 9:49 AM, Peter van Heusden wrote: > Yes, this went away with newer versions of BLAST (and BLAST+). > The 2.2.15 version is from 2006. OK, that would explain why I didn't find the issue myself during the development. > I've added test data and tests to the tool's XML file.

[galaxy-dev] Web links not leading to appropriate location anymore.

Hello, We're experiencing a major issue in the web application and don't know where to look for a potential solution: Whichever link we click on it always brigs us back to the welcome page (galaxy/root). There are a few exceptions to that: - saved histories, saved datasets and api key in the

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

Louise, I had the same problem. After hg revert -r 3ee9430186fb everything was back to normal for me. I hope this helps.. 2011/11/30 Louise-Amélie Schmitt > Hello, > > We're experiencing a major issue in the web application and don't know > where to look for a potential solution: Whichever link

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

Thanks a lot Ross, it works fine now. Best, L-A Le 30/11/2011 11:34, Ross a écrit : Louise, I had the same problem. After hg revert -r 3ee9430186fb everything was back to normal for me. I hope this helps.. 2011/11/30 Louise-Amélie Schmitt > Hello,

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

This is undoubtedly a result of something I broke in change set Commit 5db0da0007fc, so I'll get things functional again. Sorry for the problems this caused you. Ross, does your Galaxy instance have the following config setting in universe_wsgi.ini? require_login = True On Nov 30, 2011, at 5:

[galaxy-dev] extract_genomic_dna.py checks alignseq.loc?

Hi all, I recently upgraded our local instance of galaxy to the latest revision of galaxy-dist. Now I tried to use "Extract Genomic DNA" with a 3 column bed file, which only contains chr, start and end, with database/build set to hg19. First of all, running the module results in the following err

Re: [galaxy-dev] Proposed patch to blastxml_to_tabular.py

On 30/11/2011 11:58, Peter Cock wrote: > On Wed, Nov 30, 2011 at 9:49 AM, Peter van Heusden wrote: >> Yes, this went away with newer versions of BLAST (and BLAST+). >> The 2.2.15 version is from 2006. > OK, that would explain why I didn't find the issue myself > during the development. > >> I've a

Re: [galaxy-dev] Toolshed not accessible

Hi Greg, Sorry for the late reply! Yes, we see the error when trying to install a tool from the Galaxy tool sheds ('Install to local Galaxy') We are now back on yesterdays revision (3ee9430186fb) Thanks, Sajoscha On Nov 23, 2011, at 5:34 PM, Greg Von Kuster wrote: > Hi Sajoscha, > > Wh

Re: [galaxy-dev] jquery script error

Iry, Thanks for reporting this, I've just committed a fix in changeset 6346:de03f821784b. The problem was that in browsers without native JSON parsing, json2 has to be loaded for storage to function. Let me know if this doesn't resolve your issue. -Dannon On Nov 14, 2011, at 11:11 AM, Iry

Re: [galaxy-dev] extract_genomic_dna.py checks alignseq.loc?

Hi Holger, > I went to the respective file and found that the line which defines > seq_file is commented out: > (l.38 in def check_seq_file()) > ## seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR > > This seems to be a bug in the current version of the file. There is clearly something amiss

Re: [galaxy-dev] Shogun Toolbox?

Thanks Vipin. I think I understand enough for now! On Nov 28, 2011, at 3:51 PM, Vipin TS wrote: > Hi Kipper, > > Sorry I got confused, Yes you are right, both ways are fine I think. > > --Vipin > > > Vipin, > > Thanks for quick reply. Pardon my asking, as I said I am new to Galaxy > deve

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

Hello Ross and Louise-Amelie, I've just committed what I hope is a fix for this in change set 834de698004e, so when it is convenient can you check things out and let me know? If things are not yet fixed, I'll revert most of what was included in change set 5db0da0007fc, just leaving what is nec

Re: [galaxy-dev] Toolshed not accessible

I've recently added the following section to the tool shed wiki. Since you are using apache, make sure you have all of the necessary settings in community_wsgi.ini. Let me know if this is not the issue, and I'll need to see a complete paste log showing the exceptions as well as a copy of your

Re: [galaxy-dev] GalaxyCloudman + CADDSuite

Hello Marcel, In the future, please send all questions like this to the galaxy-dev mailing list, as doing so will streamline the process of getting a timely answer. I believe Enis is best able to answer your questions. Thanks! On Nov 30, 2011, at 9:29 AM, Marcel Schumann wrote: > Hi Greg, >

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

It works fine now, thanks for the fix! :) Best, L-A Le 30/11/2011 15:20, Greg Von Kuster a écrit : Hello Ross and Louise-Amelie, I've just committed what I hope is a fix for this in change set 834de698004e, so when it is convenient can you check things out and let me know? If things are no

Re: [galaxy-dev] GalaxyCloudman + CADDSuite

Marcel, After logging in as the ubuntu user, simply 'sudo su galaxy', and then make any modifications you want. If you do change the tools volume, remember to use the cloudman admin panel and select "persist changes to the file system: galaxyTools". -Dannon On Nov 30, 2011, at 9:42 AM, Gre

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

Hello Eric, > Submitted by epani...@cshl.edu > Hi all, > > I've read the Wiki page on Writing Functional Tests > (http://wiki.g2.bx.psu.edu/Admin/Tools/Writing%20Tests) and I've been looking > through test/base and test/functional and I am left with two questions: > > * Is it possible to

Re: [galaxy-dev] GalaxyCloudman + CADDSuite

Hi Marcel, It would be best to use 'galaxy' user to add any tools. To do so, after you've logged in as ubuntu user, simply execute: sudo su galaxy and you will become galaxy user. You can then make the desired modifications. Good luck, Enis On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster wrote:

Re: [galaxy-dev] Toolshed not accessible

You should not have to change things in your ini file if using the main Galaxy tool shed. On Nov 30, 2011, at 10:49 AM, Sajoscha Sauer wrote: > Now I'm confused :) > > I'm trying to use the Galaxy main toolshed (http://toolshed.g2.bx.psu.edu/), > not a local one. I guess I don't have to chang

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

Hi Greg, I appreciate your response! Thanks for clarifying the capabilities and limitations of the current functional testing framework. (BTW, did you mean "current" as in "current on galaxy-dist" or also "current on galaxy-central" ?) If I can find the time, these are areas I would be inter

Re: [galaxy-dev] GalaxyCloudman + CADDSuite

Hi Enis and Dannon, thanks for the reply. Yes, I should have tried 'sudo su' ... this works. Ok, integrating CADDSuite was no problem at all after this and everything seems to run well. However, when I create an AMI, terminate the cluster and create a new cluster using the new AMI, both /mnt

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

On Nov 30, 2011, at 11:11 AM, Paniagua, Eric wrote: > Hi Greg, > > I appreciate your response! Thanks for clarifying the capabilities and > limitations of the current functional testing framework. (BTW, did you mean > "current" as in "current on galaxy-dist" or also "current on galaxy-centra

[galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release?

Hi, I lost my Data Libraries when I updated to the latest galaxy-dist release :( What would be the best way to go about getting them back? Thanks in advance, Liisa ___ Please keep all replies on the list by using "reply all" in your mail cl

Re: [galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release?

Lisa, What release did you update from? Did you have any access restrictions on the data libraries? If so, are you logged in as a user that has those access privileges? Simply updating you Galaxy code base should not have caused this issue for you. On Nov 30, 2011, at 1:38 PM, Liisa Koski

Re: [galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release?

Sorry! They are back! I was looking at the wrong installation :( Thanks, Liisa From: Greg Von Kuster To: Liisa Koski Cc: galaxy-dev Date: 2011-11-30 13:45 Subject: Re: [galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release? Lisa, What release did you upda

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

Thanks for the quick replies again! Yeah, from a technical standpoint such support is certainly doable. My employer strongly discourages modifying the Galaxy code base too invasively (if at all), which is pretty fair since I'm not in a position to take responsibility for performing future Gala

Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Hi Jeremy, I updated to the latest galaxy-dist release and can now see the boxplots (png) files from published histories. I can see the FASTQC (html) reports too but the individual graphs within the report are missing. I will update fastqc itself and see if that makes a difference. Thanks, Liis

Re: [galaxy-dev] Can't view data files from published histories, only imported histories

Liisa, Updating FastQC won't solve this issue. You'll need to manually update galaxy-dist with this changeset to see the graphs: https://bitbucket.org/galaxy/galaxy-central/changeset/c8493a61bbea Otherwise, you can wait until the next galaxy-dist to get this changeset. Best, J. On Nov 30, 2

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

Eric, We always welcome help from the Galaxy community, so if you are interested in enhancing the Galaxy code, the best way to go about it is to create your own fork off the Galaxy central repo in bitbucket, and when you have something to contribute initiate a pull request for us to review and

[galaxy-dev] Removing nodes from a CloudMan instance

Hi galaxy-devs, Quick question: when using the cloud console on CloudMan, it's possible to add different types of nodes (large, micro, etc) to the virtual cluster using the 'Add Nodes' option at the top. I can also remove a given number of nodes using the 'Remove Nodes' option at the top. However,

Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop

Hi Enis, Jeremy, and all, Thanks so much for all your help. I have another question which I suspect is just me missing something obvious. I'm guessing that when you cloned the cluster for your workshop, you used CloudMan's 'share-an-instance' functionality? When I launch a new cluster which I wan