trivial(and I still am
> going to fox this bug), setting up an amqp (rabbitmq) server and
> configuring your galaxy instances to communicate using that is a workaround.
> On Oct 8, 2014 10:45 AM, "Ulf Schaefer" wrote:
>
>> Hi all again
>>
>> Seems I am not
classes have been defined.
---
After that it starts throwing the exception in monitor_step that I
previously posted. Has anyone seen a potentially related issue? Would an
update to the latest galaxy code help? I see there are newer versions of
SQLAlchemy available. Are they part of a newer code
etc.
> On Oct 7, 2014 11:46 AM, "Ulf Schaefer" 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
ug with multiple 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" wrote:
>
>> Dear all
>>
>> Maybe one of you c
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 an
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 name
/14 09:43, Peter Cock wrote:
> On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer 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
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 file
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
> wrote:
>> Dear all
>>
>> I have several smallish BLAST databases that I would like to provide in
>> a data library. I cre
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
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 VelvetOpti
?
Thanks
Ulf
On 22/04/14 15:26, Peter Cock wrote:
> On Tue, Apr 22, 2014 at 3:02 PM, Ulf Schaefer wrote:
>> Dear all
>>
>> I am using this control to allow the user to input multiple files:
>>
>> > label="Input VCF file(s)" />
>>
>> and I am
Dear all
I am using this control to allow the user to input multiple files:
and I am using this for loop in the cheetah code to access the control:
script.sh
...
#for $i, $input_vcf in enumerate( $input_vcfs ):
"${input_vcf}",
#end for
It appears that when a user selects many files (25
pefully the
> following one (I can build pairs via the API now, but I want to be
> able to do useful stuff with them before committing :) ).
>
> -John
>
> On Wed, Dec 18, 2013 at 2:37 AM, Ulf Schaefer wrote:
>> Dear John, dear Curtis, and all
>>
>> all that
e to start and a lot better
> than nothing. Date sort is often useful, too.
>
>
> -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:
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 tag unfortunately.
If the user just selects all files they end up in his/her history
y: send the results to a new history, for every input file
>> you will get a new history, properly named.
>>
>> Hope this helps,
>>
>> Joachim
>>
>> Joachim Jacob
>> Contact details: http://www.bits.vib.be/index.php/about/80-team
>>
>>
>>
hose validators in that second block are going to
> work with multiple="true". If you test it out and there is some
> problem, please let me know I can try to fix it.
>
> I don't know if the Galaxy team wants to start replacing these blocks
> in its tools - this change
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 in this case requires quite a bit of clicking. Is
there a more conventient way fo doing this? Maybe
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 l
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 block-co
wrote:
> On Wed, Sep 11, 2013 at 9:46 AM, Ulf Schaefer 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 possib
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
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.
Unfor
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