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:
command interpreter=bash$myScript $logFile/command
where myScript is dynamically created (as part of
On Mon, Oct 24, 2011 at 9:01 AM, Appelt, Uwe
uwe.app...@nct-heidelberg.de wrote:
Dear all,
that has probably been asked 10e6 times, however, I don't find any comments
on how to properly escape special characters in a toolxy.xml. What I want to
achieve is the following:
command
Hi Peter,
thanks a lot for your quick reply. However amp;gt; doesn't seem to work as
well. Also, I do have to admit that two different doesn't work exist.
Notations that are not accepted during parsing of toolxy.xml:
\
\\
Notations that are accepted, but don't produce any content written to
On Mon, Oct 24, 2011 at 9:42 AM, Appelt, Uwe
uwe.app...@nct-heidelberg.de wrote:
Hi Peter,
thanks a lot for your quick reply. However amp;gt; doesn't
seem to work as well. Also, I do have to admit that two different
doesn't work exist.
Notations that are not accepted during parsing of
Hi again,
yes, you're right. The problem source is something else. As soon as I specify
one of the following
command interpreter=bash$hisapWrapperScript amp;gt; $logFile/command
command interpreter=sh$hisapWrapperScript amp;gt; $logFile/command
commandbash $hisapWrapperScript amp;gt;
Dear Jennifer,
thanks for the mail, I was going through the screecasts *Processing and
analysis of 454 data in metagenomic
studieshttp://screencast.g2.bx.psu.edu/galaxy/flash/mg_screencast_1.html
*
and in the tutorial after loading the data in the second step its shows a
link short read QC and
Hi Uwe,
On Mon, Oct 24, 2011 at 10:47 AM, Appelt, Uwe
uwe.app...@nct-heidelberg.de wrote:
Hi again,
yes, you're right. The problem source is something else. As soon as I specify
one of the following
command interpreter=bash$hisapWrapperScript amp;gt; $logFile/command
command
Dear Jennifer,
Ignore my previous mail sorry i figured it out
On Mon, Oct 24, 2011 at 3:31 PM, bassanio yoursbassa...@gmail.com wrote:
Dear Jennifer,
thanks for the mail, I was going through the screecasts *Processing and
analysis of 454 data in metagenomic
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 to
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
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
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
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 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
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
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 folder
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.
I have 2
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.
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 ,
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