Re: [galaxy-dev] installing phylop

Hi Jen, Thanks for your reply. I looked at these phyloP46way-Primates datasets here : http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/primates/ They don't seem to be in bigwig format and also there is one file per chromosome. The PhyloP's add_scores.loc instructions give an impressio

Re: [galaxy-dev] installing phylop

Hi Dina, These data are available from USCS in their downloads area at http://genome.ucsc.edu. See the left side bar for the 'Downloads' link, then navigate to the genome release and track files (are clearly labeled). Best, Jen Galaxy team Jennifer Hillman-Jackson Galaxy Support and Trainin

[galaxy-dev] installing phylop

I am trying to setup PhyloP in galaxy. In the add_scores.loc file it says we need the phyloP46way.primate.bw (BigWig) file. #hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw Is there a downloadable bigwig files somewhere for hg19 that I can use? >From the instructions on bigwig, it looks li

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

Hello Peter, I've added an enhanced version of your implementation for citable URLS in the tool shed to change set revision 8720:e27d0dd12752. This is currently running on the test tool shed, and viewing repositories now displays a link like this: <> I've used the same routes you set up, so b

Re: [galaxy-dev] Can't specify workflow parameters for integer values

Hi Liisa, Thank you for reporting this bug. A fix has been committed (https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed830b4f91df79b971c5) and will be available in an upcoming release. Please let us know if you encounter additional issues. Thanks for using Galaxy, Da

Re: [galaxy-dev] File Upload doesn't generate any activity

We've also seen that same error in our startup log: == Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jo

Re: [galaxy-dev] History not updating automatically

Joachim, is your history panel still not updating or did you find a solution from the info in this thread? If not, can you post the contents of the alert/popup message? Thanks, Carl On Tue, Jan 29, 2013 at 5:26 AM, Joachim Jacob |VIB| wrote: > Hi, > > > I have a similar - but not identical issu

Re: [galaxy-dev] How to use the API when using a proxy server

I'm glad that worked, Thon. Let us know if you run into any other problems with the API in a proxy set up. Carl On Thu, Jan 31, 2013 at 7:58 PM, Anthonius deBoer wrote: > Hi Carl, > > I am using the submit and get functions from the scripts/api/common.py > > I actually found that I just n

Re: [galaxy-dev] install Galaxy in Windows (URGENT)

On Feb 1, 2013, at 11:12 AM, Peter Cock wrote: > On Fri, Feb 1, 2013 at 3:48 PM, Prasun Dutta > wrote: >> Hi Peter, >> >> Unfortunately, I am not an advanced developer in python. Although, I have >> 'Cygwin' in my system. Any heads up on that will be greatly appreciated? >> > > Cygwin is a us

Re: [galaxy-dev] File Upload doesn't generate any activity

On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold wrote: > We’ve installed a local instance of Galaxy and are having trouble with the > first step of uploading files. The only thing that will currently upload is > text pasted into the URL/Text box. > > > > Any attempt to upload a file using the

[galaxy-dev] HTML output, hide "preview" text box?

Hello, Hope this is an easy request: I've set up a tool that produces HTML output. All works great, but I was hoping that there's an easy way to remove the "preview" text box from the resulting History pane item (it currently shows the unrendered html tags)? Any help greatly appreciated! Th

Re: [galaxy-dev] File Upload doesn't generate any activity

Stephen,,, Here is your solution: In the Tools panel select "Get Data", "Upload File". You can either upload a file, or enter one or more URLs in the "URL/Text" box. Enter "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute" I am not sure what happened there but it seems

Re: [galaxy-dev] loading file into local galaxy for first time

This issue was resolved by In the Tools panel select "Get Data", "Upload File". You can either upload a file, or enter one or more URLs in the "URL/Text" box. Enter "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute" From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:gal

[galaxy-dev] Can't specify workflow parameters for integer values

Hello, I created a simple workflow with an input file and the 'Select first' tool. I wanted the value to be a parameter ${value}. I am able to save the workflow and see the little grey parameters box at the top of the workflow editor. When I try to run this workflow I get a yellow box at the top

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hi Hakeem, Let me see if I can help. First, since you are running a local install, you will want to follow our distribution new briefs, posted to our wiki here, but also sent out to the mailing lists, twitter, etc. http://wiki.galaxyproject.org/DevNewsBriefs On 2/1/13 9:51 AM, Hakeem Almabraz

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hi Jennifer, Thank you again for your help. I am totally newbie to Galaxy so my issues could be due to my experience with it but I am getting some progress slowly though. Now, I am having totally different problem right now. I am trying to load simple file using the Galaxy GUi but it keeps

[galaxy-dev] February 2013 Galaxy Update

Hello all, The February 2013 Galaxy Update is now available at http://wiki.galaxyproject.org/GalaxyUpdates/2013_02 *Highlights:* - Three new public Galaxy servers -

Re: [galaxy-dev] How do I allow a large group of users to RUN my workflow without them having to make a local copy

> It seems strange not to be able to share workflows with groups if you can > share them with individual users.. The group/role system for data libraries and the sharing system for other assets were developed concurrently. It would be reasonable (and probably not that difficult) to add groups to t

[galaxy-dev] File Upload doesn't generate any activity

We've installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It's as if the

Re: [galaxy-dev] install Galaxy in Windows (URGENT)

Hi Peter, Unfortunately, I am not an advanced developer in python. Although, I have 'Cygwin' in my system. Any heads up on that will be greatly appreciated? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

Re: [galaxy-dev] loading file into local galaxy for first time

I just looked at the paster.log file while trying to load one small fasta file using Upload File or Data Library options. Here is the log I keep seeing repeating every second. 10.7.10.201 - - [01/Feb/2013:10:46:21 -0500] "POST /library_common/library_item_updates HTTP/1.1" 200 - "http://10.7.

Re: [galaxy-dev] Error loading a BAM file -- dataset needs grooming

Thanks for the response. Samtools was installed, but there was an issue with it running on our cluster versus locally. Our sysadmin has temporarily disabled the calls to the cluster until he can work out those issues. It works fine now that it's running locally. Regards, Maureen On 1/30/13

Re: [galaxy-dev] install Galaxy in Windows (URGENT)

On Fri, Feb 1, 2013 at 3:48 PM, Prasun Dutta wrote: > Hi Peter, > > Unfortunately, I am not an advanced developer in python. Although, I have > 'Cygwin' in my system. Any heads up on that will be greatly appreciated? > Cygwin is a useful system for running Unix/Linux tools under Windows, and acco

[galaxy-dev] loading file into local galaxy for first time

Hi, I just finished installed a local galaxy. I tried to load a simple small fasta file using Load Data and it is still showing as Queued (Blue). It should not take it that much to load. SO I assumed I have some issues in my installation. Can someone tell me what could ne the issue? Or how

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hi Hakeem, The set up for samtools looks correct. If the problems that you had with BWA/Bowtie were due to an error in our wiki, please send in the suggested changes to me. We want this to be correct. For the SAM->BAM tool - in the UI, there will never be a list of genomes - that is not one

Re: [galaxy-dev] install Galaxy in Windows (URGENT)

On Fri, Feb 1, 2013 at 2:33 PM, Prasun Dutta wrote: > Hi, > > I have Windows Vista and 8 in two separate laptops. I need to install a > local version of Galaxy server in both the systems. I am unable to > understand or follow the instructions given in your website > (http://wiki.galaxyproject.org/

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Thank you Jennifer for your help. I already resolved the issues with Bwa and Bowtie. I was misled with some missing instructions but I managed to resolved them by searching online. Now I am stuck at the SAM Tools displaying a reference genome :)... I will give more details at what

[galaxy-dev] install Galaxy in Windows (URGENT)

Hi, I have Windows Vista and 8 in two separate laptops. I need to install a local version of Galaxy server in both the systems. I am unable to understand or follow the instructions given in your website (http://wiki.galaxyproject.org/Admin/Get%20Galaxy). Could you kindly help me or just explai

Re: [galaxy-dev] How do I allow a large group of users to RUN my workflow without them having to make a local copy

Thon: You can share a workflow through a URL, which you can send to all members of the group. anton Anton Nekrutenko http://www.galaxyproject.org On Jan 31, 2013, at 10:52 PM, Anthonius deBoer wrote: > Hi, > > I am trying to build some workflows for people that are part of a group and I >

Re: [galaxy-dev] How to call a cgi web page in a galaxy folder from a script?

Hello James, Thank you for your answer. I use open authentication and my script now is in a local server. I call this script from user.py (in lib/galaxy/webapps/galaxy/controllers) and return to me the email of a user in other platform. My script is auth.py (in local server, cgi enable to run in a

Re: [galaxy-dev] Patch for RepeatMasker.xml for RepeatMasker 3.3.0

Hi Simon, thank you for your contribution. I updated the toolshed version to 0.1.1 with your changes. Ciao! Bjoern > Dear Galaxians, > > We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is > the expected version, as I can't find any statement about what is required in