Re: [galaxy-user] problem running Augustus
Hi Claudio, I will have a look at it, at latest tomorrow, promised. Cheers, Bjoern (Augustus wrapper developer) I am trying to use the genome Annotation tool Augustus on my locally installed copy of Galaxy. After loading the data file, all analyses stop and deliver the following: error an error occurred with this dataset: /bin/sh:1:augustus: not found python: can't open file: '/extract_features.py': [Errno 2] No such file or directory Python is installed on my system (Ubuntu 12.04, Python 2.7.3) It must be something very basic I'm missing, but more basic are my linux skills… Thanks a lot Claudio ~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^ Claudio Slamovits, Canadian Institute for Advanced Research Department of Biochemistry and Molecular Biology Dalhousie University 5850 College Street, Halifax, Nova Scotia B3H 4R2, Canada Lab Webpage: http://slamo.biochem.dal.ca Lab: (902) 494 7894 Office: (902) 494 8825 Fax: (902) 494 1355 ^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~ Reality is what it is, not what you want it to be. - Frank Zappa ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
Re: [galaxy-user] Fwd: About empty no peek problem
Hi Xiao,
the attached ones are working for me, hope for you too.
Cheers,
Bjoern
Dear Bjorn
The configure xml file and the relevant R scripts is attached.
Thank you for all your help.
Regards,
XiaoTao
The University of HongKong
2013/9/3 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de
Hi Xiao,
can you show us the complete wrapper XML script?
Thanks,
Bjoern
-- Forwarded message --
From: XiaoTao Jiang biofuture.ji...@gmail.com
Date: 2013/9/2
Subject: About empty no peek problem
To: galaxy-user-requ...@lists.bx.psu.edu
Dear all
Today I embed one of my R script into local galaxy, I have
encountered
a strange problem. The script can successfully in local.
However,
when I run it online in galaxy, the output file is empty and
in
history panel, it display empty and no peek.
I searched the mailing list, but still can not find
solutions to solve
it.
The command display in sever is : key part
galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,297
executing: R
CMD BATCH --slave
--args
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat
barchart.r
galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,493
execution
finished: R CMD BATCH --slave
--args
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat
barchart.r
galaxy.jobs DEBUG 2013-09-02 17:29:49,538 Tool did not
define exit
code or stdio handling; checking stderr for success
galaxy.tools DEBUG 2013-09-02 17:29:49,697 Error opening
galaxy.json
file: [Errno 2] No such file or directory:
'/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/job_working_directory/000/71/galaxy.json'
galaxy.jobs DEBUG 2013-09-02 17:29:49,759 job 71 ended
I check the generated output file
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat
It is empty zero in size
and then I run the command in local command
R CMD BATCH --slave
--args
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat
/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat
barchart.r
The output is correct.
Any suggestions will be appreciated !!
Xiaotao JIANG
Regards,
The University of HongKong
Department of Civil Engineering
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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local Galaxy instances and the Galaxy source code, please
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argsall - commandArgs()
input - argsall[6]
output - argsall[7]
tabl - read.table(file=input, header=TRUE, sep=\t)
fac - levels(tabl[,2])
#fac
#length(fac)
ini - rep(0,length(fac))
#for (q in 1:length(fac)) {
# ini[q] - 0
#}
#ini
for (i in 1:length(tabl[,2])) {
for( j in 1:length(fac) ){
if(tabl[,2][i] == fac[j]){
ini[j] - ini[j] + tabl[,3][i]
}
}
}
figureformat - fi.pdf
pdf(figureformat)
par(mar=c(5,12,4,2))
barplot(ini, names.arg=fac,col=red, width=0.2, axis.lty=0, las=2,
xlab=Frequence of ARGs, main=Bar Plot of ARGs Class, cex.axis=1,
cex=0.7,offset=0, font=2, adj=0, horiz=T,border=NA, density=NA)
dev.off()
file.copy(figureformat, output,
Re: [galaxy-user] Galaxy Tool Version Question
Hi Scott, please click on the 'i' info icon in one of your datasets (next to the download button) you will find many additional information's, including the wrapper version and the version of the underlying tool. Cheers, Bjoern To Whom it May Concern, I was trying to find the version information regarding certain RNA-Seq analysis (Tophat, Tophat2, Cufflinks), and have had difficulty finding the versions for either Tophat instance. Is there a way to find out what version of Tophat is being used? Thank you for your time, Scott Nixon ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
[galaxy-user] Join the HOMER Galaxy wrapper development!
Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc files to define different HOMER datasets - macros - compostite datatypes (html output) I think that project can be a good start to learn Galaxy Tool development with all its simple and enhanced features. Also HOMER is a complex suite and you can add small and really big features if you like. If you are interested but did not have any experience in Tool development, do not hesitate to ask. I will try to help and explain as much as I can. For the beginning I included only 3 tools, and only one of them with a bunch of parameters. So there are many things to do ... If anyone is interested in leaning Galaxy Tool development and want to contribute. Fell free to join and contact me. Cheers, Bjoern P.S. I do not mind to merge my changes to the already existing repository from Kevin, but I was not able to contact him. http://toolshed.g2.bx.psu.edu/view/kevyin/homer ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
Re: [galaxy-user] Illumina Methylation tool in toolshed
Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
Re: [galaxy-user] Illumina Methylation tool in toolshed
Not that I know of, mine is wrapping IMA. cheers, Bjoern Hi Bjoern, Thank you for your reply. To be precise I am looking for a wrapper of * lumi. *http://www.bioconductor.org/packages/2.12/bioc/html/lumi.html Do we have that in main tool shed or test tool shed or in github? Thanks, Sachit On Mon, Jul 29, 2013 at 2:53 PM, Bjoern Gruening bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
