. Are they part of a newer code base?
Thanks a lot for your help
Ulf
On 07/10/14 12:20, Ulf Schaefer wrote:
Update:
The usual switching it off and on again (server reboot) has resolved the
problem (for now), albeit in a rather unsatisfactory manner.
If there are any insights what caused
(rabbitmq) server and
configuring your galaxy instances to communicate using that is a workaround.
On Oct 8, 2014 10:45 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Hi all again
Seems I am not so fortunate that this would just go away.
It appear to be happening sometimes at start-up time for one
Dear all
Maybe one of you can shed some light on this error message that I see in
the log file for one of my handler processes. I get about one of them
per second. The effect is that most of the jobs remain in the waiting
to run stage.
The postgres database is running on a separate server and
mapper initialization that I haven't been able to
reproduce yet, so any information will help. Database configuration,
number of processes, etc.
On Oct 7, 2014 11:46 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
Maybe one of you can shed some light on this error message that I see
AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
Maybe one of you can shed some light on this error message that I see in
the log file for one of my handler processes. I get about one of them
per second. The effect is that most of the jobs remain in the waiting
to run stage
Dear all
For each bam file in my history I can download the associated bai (bam
index) file.
I assume these files are stored somewhere under
/mount/galaxy/database/files/_metadata_files. Correct? Is there an easy
way to find the bam index file for a bam file, given only the internal
file
/14 09:43, Peter Cock wrote:
On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Nate, dear Peter
Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If
I try to get the data out of the library into anothre history
Dear Nate, dear Peter
Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If
I try to get the data out of the library into anothre history, I am
successful for the html but not for the blastdb. The problem seems to be
that the primary data
Dear all
I have several smallish BLAST databases that I would like to provide in
a data library. I create them in a history with the makeblastdb tool and
them try to add them to the library. I see that for each blast db there
is an empty file created (like /path/dataset_12345.dat) and a folder
not check for size 0 at the time of
importing it.
Thanks
Ulf
On 23/07/14 10:56, Peter Cock wrote:
On Wed, Jul 23, 2014 at 10:47 AM, Ulf Schaefer ulf.schae...@phe.gov.uk
wrote:
Dear all
I have several smallish BLAST databases that I would like to provide in
a data library. I create them
Hi all
We frequently use the syntax below to rename outputs of workflows that
we run in batch. It is convenient to have sample names from fastqs
carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g.
the
Dear all
I am using this control to allow the user to input multiple files:
param name=input_vcfs type=data multiple=true format=vcf
label=Input VCF file(s) /
and I am using this for loop in the cheetah code to access the control:
command interpreter=bash
script.sh
...
#for $i, $input_vcf in
?
Thanks
Ulf
On 22/04/14 15:26, Peter Cock wrote:
On Tue, Apr 22, 2014 at 3:02 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
I am using this control to allow the user to input multiple files:
param name=input_vcfs type=data multiple=true format=vcf
label=Input VCF file(s) /
and I am
.
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John Chilton
Sent: Tuesday, December 17, 2013 4:03 PM
To: Ulf Schaefer
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] sort list of ftp uploaded files
If Galaxy just
before committing :) ).
-John
On Wed, Dec 18, 2013 at 2:37 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear John, dear Curtis, and all
all that is required to fix my current issue is that the files show up
in the 'Upload File' tool form in alphabetical order.
I assume that at some point
Dear all
Is there a way to sort the list of files that a user has uploaded via
FTP? Currently they appear on the form of the tool 'Upload File' in
random order it seems. There is not much documentation on the param
type=ftpfile / tag unfortunately.
If the user just selects all files they end
this helps,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 10/01/2013 02:27 PM, Ulf Schaefer wrote:
Dear all
We frequently find ourselves in situations where a tool needs to be run
with a lot of input files. For example, run the GATK UnifiedGenotyper
Dear all
We frequently find ourselves in situations where a tool needs to be run
with a lot of input files. For example, run the GATK UnifiedGenotyper
with easily dozens of bam files.
Using the repeat in this case requires quite a bit of clicking. Is
there a more conventient way fo doing
of data blocks going forward. They are working out
great for us on Galaxy-P though.
-John
On Tue, Oct 1, 2013 at 7:57 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Oct 1, 2013 at 1:27 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
We frequently find ourselves
Dear Jeremy
Thank you for your reply and sorry for not being clear. In short I
solved the problem. Below is some info, in case this is useful for
someone else.
Thanks for your help
The situation was:
On Main:
Visualisation of the SAM/BAM file - OK
Visualisation of the VCF file - OK
On my
Hello all
Has anyone successfully integrated the phylib file type into Galaxy in
their local install? It's a standard file type for multiple sequence
alignment and I could not possibly be the only one who want to support
it in a local install.
I saw the instructions on the wiki for adding new
wrote:
On Wed, Sep 11, 2013 at 9:46 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Hello all
Has anyone successfully integrated the phylib file type into Galaxy in
their local install? It's a standard file type for multiple sequence
alignment and I could not possibly be the only one who want
Dear all
My attempts to visualise a vcf file in trackster fail. I can visualise
the corresponding SAM/BAM files fine. I can visualise the same file on
Galaxy main too, but not in my local install.
I receive the following error message:
Trackster Error
Input error: found interval with
Hello all
It was indicated in several recent posts (e.g. there
http://dev.list.galaxyproject.org/support-pbkdf2-in-proftpd-1-3-5rc3-td4660836.html)
that for Galaxy to reliably work with ProFTPD, it is recommended to
disable the new PBKDF2 encryption of passwords and revert back to SHA1.
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