[galaxy-user] tool.xml "&>" console redirection within command-tag

Dear all, that has probably been asked 10e6 times, however, I don't find any comments on how to properly escape special characters in a toolxy.xml. What I want to achieve is the following: $myScript &> $logFile where myScript is dynamically created (as part of the configfiles-section) and the

Re: [galaxy-user] tool.xml "&>" console redirection within command-tag

On Mon, Oct 24, 2011 at 9:01 AM, Appelt, Uwe wrote: > Dear all, > > that has probably been asked 10e6 times, however, I don't find any comments > on how to properly escape special characters in a toolxy.xml. What I want to > achieve is the following: > > $myScript &> $logFile > > where myScript

Re: [galaxy-user] tool.xml "&>" console redirection within command-tag

Hi Peter, thanks a lot for your quick reply. However "&>" doesn't seem to work as well. Also, I do have to admit that two different "doesn't work" exist. Notations that are not accepted during parsing of toolxy.xml: &> \&> \\&> Notations that are accepted, but don't produce any content written

Re: [galaxy-user] tool.xml "&>" console redirection within command-tag

On Mon, Oct 24, 2011 at 9:42 AM, Appelt, Uwe wrote: > Hi Peter, > > thanks a lot for your quick reply. However "&>" doesn't > seem to work as well. Also, I do have to admit that two different > "doesn't work" exist. > > Notations that are not accepted during parsing of toolxy.xml: > &> > \&> > \\&

Re: [galaxy-user] tool.xml "&>" console redirection within command-tag

Hi again, yes, you're right. The problem source is something else. As soon as I specify one of the following $hisapWrapperScript &> $logFile $hisapWrapperScript &> $logFile bash $hisapWrapperScript &> $logFile sh $hisapWrapperScript &> $logFile I get a according debug-line in the galaxy.log, re

Re: [galaxy-user] analysis of 454 data

Dear Jennifer, thanks for the mail, I was going through the screecasts *Processing and analysis of 454 data in metagenomic studies * and in the tutorial after loading the data in the second step its shows a link short read QC and m

Re: [galaxy-user] tool.xml "&>" console redirection within command-tag

Hi Uwe, On Mon, Oct 24, 2011 at 10:47 AM, Appelt, Uwe wrote: > Hi again, > > yes, you're right. The problem source is something else. As soon as I specify > one of the following > > $hisapWrapperScript &> $logFile > $hisapWrapperScript &> $logFile > bash $hisapWrapperScript &> $logFile > sh $his

Re: [galaxy-user] analysis of 454 data

Dear Jennifer, Ignore my previous mail sorry i figured it out On Mon, Oct 24, 2011 at 3:31 PM, bassanio wrote: > Dear Jennifer, > thanks for the mail, I was going through the screecasts *Processing and > analysis of 454 data in metagenomic > studies

Re: [galaxy-user] tool.xml "&>" console redirection within command-tag

Well, no, I didn't try to specify neither an "interpreter=" nor the actual shell-binary as part of the command-tag itself, because I'm assembling the shell-script dynamically within a configfile-tag. Thus, I do not see any chance to apply an "executable"-flag to that script that is infact filed

[galaxy-user] Permissions and private roles

Hi all I¹m trying to get my head round permissions on Data Libraries. I have a couple of questions 1) When I come to give access to a library the only roles I see are the current (admin) user¹s private roles and other non-private roles I have created - no other private roles. Reading the wiki page

Re: [galaxy-user] Permissions and private roles

Hello Anthony, On Oct 24, 2011, at 6:55 AM, Anthony Underwood wrote: > Hi all > > I’m trying to get my head round permissions on Data Libraries. I have a > couple of questions > 1) When I come to give access to a library the only roles I see are the > current (admin) user’s private roles and o

[galaxy-user] Permissions and private roles

Hi all I¹m trying to get my head round permissions on Data Libraries. I have a couple of questions 1) When I come to give access to a library the only roles I see are the current (admin) user¹s private roles and other non-private roles I have created - no other private roles. Reading the wiki page

[galaxy-user] Sequences are not currently available for the specified build

Hi all, We are just beginning to analyze RNA-seq data and hope to make use of the Galaxy tools. We are not using a commonly studied organism such as human. Rather, our data are from the bacterium Pseudomonas fluorescens Pf0-1. The genome for P. fluorescens Pf0-1 appears in the "database/build" men

Re: [galaxy-user] Permissions and private roles

Hello Anthony, On Oct 24, 2011, at 10:01 AM, Anthony Underwood wrote: > Hi Greg > > Thanks for the reply. I can see now that as an admin user I can now add > private roles using the Admin View as opposed to the data libraries view. > It is still a bit unclear how a folder can be visible to one

[galaxy-user] Removing low quality reads

Galaxy Users, I would like to filter a .bam file to remove reads with low mapping quality, especially ambiguously mapped reads (MAPQ = 0). I can easily do this using the command line version of samtools as shown below. samtools view -bq 20 hba1.bam > hba1_MAPQ20.bam None of the options available

Re: [galaxy-user] Permissions and private roles

Hi Greg Thanks for the reply. I can see now that as an admin user I can now add private roles using the Admin View as opposed to the data libraries view. It is still a bit unclear how a folder can be visible to one user but not to another. If both users have access to the library then they can vi

Re: [galaxy-user] Permissions and private roles

> Thanks for the reply Greg > > Still don¹t think I¹ve quite got it in my head though it¹s becoming clearer. > > I have 2 users each whom I have given permission to access 2 datasets. > > user 1 has access to data in a folder called 1st result and user 2 has access > to data found in both a fold

Re: [galaxy-user] Permissions and private roles

I'm not following you here - please decipher your folder names, which I assume are mapped to your encoded request strings. On Oct 24, 2011, at 1:27 PM, Anthony Underwood wrote: >> Thanks for the reply Greg >> >> Still don’t think I’ve quite got it in my head though it’s becoming clearer. >> >>

Re: [galaxy-user] Permissions and private roles

>> Also another question about permissions. If I create a Galaxy page and share >> that with limited users then it appears that the datasets are all public via >> a URL is that correct? Yes, all datasets are public via URL by default in Galaxy, and a Galaxy Page makes it easy to find this URL.

[galaxy-user] Extract genomic DNA-strand information is not recognized

Hello, I am trying to extract sequences from a FASTA file containing genomic information. The coordinates are in a tab-delimited format, which is recognized as BED format by Galaxy (meaning that the 6th column is correctly interpreted as 6. Strand). However, upon running "Fetch sequences" , Ex