Branden,
Sorry for the delay in response. Have you gotten things working yet?
If not, what changeset are you on now? The data tables issue is what's
going on here. But it's odd that you're still seeing "from_file" in
BWA and Bowtie, because they (plus all NGS tools except the samtools
one
Amir,
Uploading a BAM file in Galaxy requires the Samtools package. You can
download it from http://samtools.sourceforge.net/, but if you want
more information about installing it (and other NGS tools) in Galaxy,
see our wiki page: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSe
Holger,
That particular tool uses a different loc file--all_fasta.loc, which
is simply a list of fasta files with full path/name. Are your other
Picard tools working? Let us know if you run into further issues.
Thanks,
Kelly
On Fri Jun 24, at 7:44 AM, Holger Klein wrote:
Dear all,
I ha
Peter,
This loc file is tab-separated, but it's just that one of its columns
(the third, which holds the Galaxy formats that the line applies to)
can hold comma-separated values. For instance, you could have the line:
hg18_standard hg18 fastqsanger,fastqcssanger hg18 standard indexes /
data/
Henry,
I'm moving this over to galaxy-dev since it has to do with a local
instance.
It definitely sounds like you've got things set up right. You don't
say what the result of your run is--is it "successful" (green) but an
empty file? Or is there an error? If it's empty, it's possible your
Shashi,
All of Galaxy's datasets have the extension ".dat" so your problem is
not uncommon. The general solution to this is to create temp files
that have the the required extensions for the tool and point them to/
from the actual Galaxy input and output. There are several ways to do
this.
Dave,
The fact that the Tophat wrapper was not setting the genome based on
the alignment genome was actually a bug, but I just fixed it in
changeset 5570:0c1251f25c6b.
Let us know if you have further questions.
Regards,
Kelly
On May 17, 2011, at 10:57 AM, Dave Walton wrote:
I'd like to
That opening-the-entire-file inefficiency in our sam_to_bam.py was
fixed quite some time ago (4/30/2010, in 3724:007f175c8b88). It has
used getsize since then. It's really just intended to catch weird
errors that don't throw an actual error (also, I think that if the sam
file has no header,
Hello,
Please see the wiki page https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
.
Let us know if you have further questions.
Regards,
Kelly
On Mar 21, 2011, at 1:08 PM, blake haas wrote:
Dear Galaxy,
I had galaxy installed locally, and when I try running tophat, there
is
Nicki,
You are right that Galaxy's Bowtie only allows one input fastq. You
would have to combine your multiple input files into one before
running it in Galaxy. You can do this with the Concatenate datasets
tool (under Text Manipulation).
Let us know if you have any further questions.
Re
(I'm redirecting this to the galaxy-dev list, which is more
appropriate since it's about a local installation.)
Begin forwarded message:
From: Nick Schurch
Date: February 9, 2011 7:17:45 AM EST
To: galaxy-u...@lists.bx.psu.edu
Subject: [galaxy-user] operating on, and getting at, large files
Hi,
There are two things: first, the Bowtie for Illumina and Bowtie for
SOLiD wrappers use different data tables (bowtie_indexes as opposed to
bowtie_indexes_color), which refer to different loc files
(bowtie_indexes.loc and bowtie_indexes_color.loc, respectively).
Secondly, although this
Hi,
What type of data are you trying to add? For NGS references, see https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
. Let us know if that isn't enough info.
Regards,
Kelly
On Feb 2, 2011, at 3:58 PM, Geoff Jentry wrote:
Hello ...
I've installed a Galaxy server on one of o
Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which
tools to load. Note that functional tests use tool_conf.xml.sample,
and we leave the EMBOSS tools commented out in that file, so your
tool_conf.xml file will still have them commented out if you haven't
changed tha
outdated. I am running 0.12.1 currently.
--
Branden Timm
bt...@glbrc.wisc.edu
On 1/13/2011 12:30 AM, Kelly Vincent wrote:
Branden,
Which revision of Galaxy are you using? What this sounds like is
that it is taking a long time to set the metadata on the resulting
SAM file, i.e., after the
Branden,
Which revision of Galaxy are you using? What this sounds like is that
it is taking a long time to set the metadata on the resulting SAM
file, i.e., after the Bowtie job has run. Prior to 4698:48a81f235356
(12/1/10), all the lines in a large SAM file would be read to
determine how
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