Re: [galaxy-dev] Tool dependency installation fail, any documentation?

Dave, It's : hg log | head changeset: 8153:5dcbbdfe1087 tag: tip user:Daniel Blankenberg date:Tue Nov 06 12:57:23 2012 -0500 summary: Allow rerun to access hidden datasets. Thanks, Franco On 12/12/12 3:13 PM, "Dave Bouvier" wrote: > Franco, > > You're right,

Re: [galaxy-dev] Tool dependency installation fail, any documentation?

Franco, You're right, I see a both clean and all rules in the makefile. It looks almost like it's not finding the expected makefile, I'll have to look into that in the morning. As for the download_by_url action, it downloads and extracts the specified file, then changes to the extracted direc

[galaxy-dev] pbs_python and torque 4.x

Hi all, We are trying to get our instance of Galaxy submitting jobs to a cluster a using the staged method referred to at http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Our cluster is running Torque 4.1.3. We need to use Torque 4.x clients to be able to submit jobs to it. I

[galaxy-dev] Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries

Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galax

Re: [galaxy-dev] Tool dependency installation fail, any documentation?

Hi Dave, It does not require it, but it should not fail either as the clean rule is in the makefile.. By removing it I get: make: *** No rule to make target `all'. Stop. Same problem as before but this time with the 'all' rule... I'm not sure what the wrote: > Franco, > > BEDTools, unlike some

Re: [galaxy-dev] Tool dependency installation fail, any documentation?

Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file f

[galaxy-dev] Tool dependency installation fail, any documentation?

Hi list, I got the following tool_dependencies.xml file failing:             http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz make clean make all bin $INSTALL_DIR/bin    $INSTALL_DI R/bin

Re: [galaxy-dev] [galaxy-bugs] galaxy.genenetwork.org

有olb吃掉 Yunbo Xu 817 Hickman rd, Apt A-23 Augusta,GA 30904 706 - 877 3892 On Dec 11, 2012, at 4:13 PM, Lei Yan wrote: > Dear Dannon and James, > > On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker wrote: > > • I installed a Cloud Galaxy instance one month ago, and a user > > reported that i

[galaxy-dev] Job is waiting to run

I have a local galaxy server, and I built a workflow, it got stuck in one step in the middle. The computer is a 64 cores server, and no other jobs running in this server. Any idea how to trouble shooting? Thanks, Fenglou ___ Please keep all r

[galaxy-dev] Installing Job Runners on a Cluster

Hi all, I could use some help getting DMRAA to run. We already have a galaxy instance with pbs running, but I'd like to connect to Torque using dmraa because we eventually intend to port over to a different resource manager. I've followed these instructions: http://apps.man.poznan.pl/trac/pbs-

Re: [galaxy-dev] Impersonate a User

Hi Greg, Try clicking the logout button. That should logout of the user you are impersonating and back into you. Although, this does have a few quirks also and may log you right out. Don't forget that when you are impersonating someone the history may not be automatically loaded and you will have

[galaxy-dev] problem with uploading data

Hi Nate, I loaded the file named s_6_1_sequence.txt.gz (Illumni file) under the login name abdul.ban...@uconn.edu as FTP. Whenever I am trying to load it as history so that I can run it for analysis, the file upload is showing error and massage come

[galaxy-dev] Extra files saved outside of Galaxy's history?

Hi all, I have a pipeline involving a series of scripts, which creates directories (and many subdirectories), that I'd like to wrap for use in Galaxy. Although the contents of the folders are not the primary output of the pipeline, (and I don't want them as history items), I'd still like them t

Re: [galaxy-dev] Re-installing error persists

Hi Franco, I'm not quite sure what page you'r eon, but if you're looking at the page that has the tool dependency with the error status, you should be able to click the link of the tool dependency and see the error, log, etc. If this is not the page you're referring to, then I'll have to take

[galaxy-dev] Impersonate a User

Hi guys, I tried the impersonate a user feature, but I don't know how to stop impersonating a user? I tried going back to the impersonate a user feature and selecting myself but it's not clear if it changed anything, and I no longer see the History items I had before I did the impersonation. Tha

[galaxy-dev] Downloading datasets without username/password when login is required

Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this a

[galaxy-dev] Mutation/SNP detection RNA-Seq

Hi, I am trying to look mutations/SNPs in RNA-Seq data. Can anyone suggest me a workflow in Galaxy on how to detect SNPs and mutations Thanks in advance Suz ___ Please keep all replies on the list by using "reply all" in your mail client.

Re: [galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

Dannon, Here is myjavascript console errors : SyntaxError: missing ) after argument list : /* ool( 'sm_miRNA_join_annot', '* Construction de la matrice d'annotations' ) */ /*editor...8829fc# (ligne 1, col. 60)*/ I replaced this syntax "Construction de la matrice d'annotations" by the latter

Re: [galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

The paster.log is just the file for the output you've copied below when running daemonized -- if you're running in the foreground it just gets sent there instead of to the file. So, no obvious errors there. Could you check for javascript console errors? And, if you'd like, feel free to send t

Re: [galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] "GET /galaxy/workflow HTTP/1.1" 200 - "http://URL/galaxy/root"; "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:11 +0200] "GET /

Re: [galaxy-dev] [SPAM] Re: About the output

my phthon file: gf = open('showme.txt', 'w') gf.write('this is a test text') gf.close print "info" my xml file:   table browser proxy       test.py               I clicked the "!"  button, it shows : Tool: Tool1 Name: Tool1 Created: Dec 11, 2012 Filesize: 0 bytes Dbkey: ? For

Re: [galaxy-dev] [SPAM] Re: About the output

On 12/11/2012 03:49 PM, Chenhao Li wrote: Thx Hans-Rudolf But I did write in the xml file Here is just a mistake In ~in ~/database/files/ folder there is just a folder named 000 and there are lots of *.dat file in 000 folder I assume, the latest *.dat file is the txt file you are interest

Re: [galaxy-dev] About the output

Thx Hans-Rudolf But I did write in the xml file Here is just a mistake In ~in ~/database/files/ folder there is just a folder named 000 and there are lots of *.dat file in 000 folder From: Hans-Rudolf Hotz To: Chenhao Cc: galaxy-dev@lists.bx.psu.edu Se

Re: [galaxy-dev] Installation issue on EC2

Hi, Dannon. Thanks for the tip. No, I was not reusing the cluster names exactly to avoid previous data to mess up with my fresh new deployments. There were indeed about 8 buckets referring to clusters that don`t exist anymore. Write now I can`t remove my current cluster by the w

Re: [galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman wrote: > Hello, > > For one of my tools that I have added to my local instance of Galaxy, I can > not add this tool in the editing workflow. When I click on the tool na

[galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman

[galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench

Re: [galaxy-dev] Public Tool Shed Error

Hello Adam, Thanks for reporting this. It was fixed in a change set 10 days ago that just missed the cutoff of the last Galaxy distribution release. The fix is currently running on the test Galaxy tool shed and will be applied to the main Galaxy tool shed with the next Galaxy distribution rel

[galaxy-dev] Public Tool Shed Error

Hi, I have been using the tool shed recently and come across a problem. When a searching for valid tools within the Public Tool Shed, it seems that if the search should return nothing found, it is instead displaying a Server Error page instead. For example: http://toolshed.g2.bx.psu.edu/reposi

[galaxy-dev] some problem with the fastq interlacer

Hi all,   I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer seems do not reganize the name of the pair-end reads, and treat the pair-end reads as non-pair-edn reads.   Best regards___ Please keep all replies on the l

Re: [galaxy-dev] Displayed versions of tools in Galaxy

This has been confusing for me also. Perhaps if we had a way to distinguish between the two by prefixing the tool version of a wrapper with "w0.0.5" and the actual tool version with "v1.3.0"? I think that Galaxy determines the versions of the tools it loads at startup in lib/galaxy/tools/__init__.

Re: [galaxy-dev] Trying to Run MegaBlast

On Monday, December 10, 2012, Jeremy Goecks wrote: > > > Decompress and unpack the file and you'll find the relevant files (though > everything now has extensions with p* rather than n*); add an entry to > blastdb pointing to the directory with these files and you should be good > to go. > > J.

[galaxy-dev] Displayed versions of tools in Galaxy

Hi guys, I wasn't sure if I should send this one to galaxy-user. I have just confused myself about the versions of tools displayed within Galaxy. If I select the TopHat tool, the tool UI says "Tophat for Illumina (version 1.5.0)". After I have run the job, the step panel in the History window say

Re: [galaxy-dev] About the output

On 12/10/2012 11:26 PM, Chenhao wrote: I made a galaxy tool which is just create a txt file. When I use this tool , I wish to let it show the detail of the txt. In the xml file I use : I assume, this should be written: I am surprised, your tool doesn't create an error much earlier.