ny new cluster will work fine.
>
> Cheers.
>
> On Tue, Sep 1, 2015 at 7:42 PM, Alexander Vowinkel <
> vowinkel.alexan...@gmail.com> wrote:
>
>> Update:
>>
>> ProFTP gives as an answer to passive mode the INTERNAL IP to connect
>> which mak
Hi,
when downloading/exporting a history via the interface,
visible collections are not being exported.
The contents of the collection(s) are hidden,
the Colleciton itself is visible.
Best,
Alexander
___
Please keep all replies on the list
,
Alexander
2015-09-01 18:19 GMT-05:00 Alexander Vowinkel <vowinkel.alexan...@gmail.com>
:
> Hi,
>
> I get the error "Could not read from socket: ECONNRESET - Connection reset
> by peer" when connecting with FileZilla to the Cloud Instance.
> Using launch.usegalaxy.org
>
&g
Hi,
I have a big problem here.
Jobs that are cancelled by slurm appear to galaxy as finished normally.
For me this is especially bad because all following workflow steps
go on working with corrupted/empty/whatever data.
in the job stderr I can find:
slurmd[w4]: *** JOB 194 CANCELLED AT
Hi,
can someone tell me something about this?
Pointing at the runner stated in the log vs. expected runner.
Thanks,
Alexander
2015-07-06 18:08 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi,
I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml:
I added a destination
by some people from the slurm-drmaa
community too.
Patches are available, but not included in a release.
Best,
Alexander
2015-07-31 11:38 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi,
can someone tell me something about this?
Pointing at the runner stated in the log vs
Hi,
I am referring to this:
http://dev.list.galaxyproject.org/CloudMan-auto-scaling-Use-spot-instance-for-worker-node-tp4665813p4665835.html
I would give an upvote for spot instances for auto-scaling.
Have there been more ideas about this since?
Best,
Alexander
I did the runs now just in a single history.
the collections are empty (I checked also in the API)
2015-07-15 18:49 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi,
I have this tool that creates a collection by discovery datasets.
It always worked fine, but this time I had 3
Hi guys,
cloudlounch at launch.usegalaxy.org doesn't work for me anymore.
Some hours ago I still was able to start a cluster, but now it seems
that the launcher can't connect to my amazon anymore?
No machnie get's started.
But I'm still able to fetch key pair and placement.
Any suggestions what
, Jul 13, 2015 at 5:06 PM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi,
I get this error on cluster creation:
Error creating volume: EC2ResponseError: 400 Bad Request
InvalidParameterValueVolume of 2048GiB is too large for volume type
standard; maximum is 1024GiB
Is there a way
Hi,
I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml:
I added a destination with following param:
param id=nativeSpecification-N1 --cpus-per-task 1
--mem-per-cpu=4G/param
Galaxy service was restarted after chaning this.
Now I get the error Unable to run job due to a misconfiguration of
, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi Enis,
I am trying to launch my cloudman instance with this launcher again:
https://launch.usegalaxy.org/launch
You created the flavor for me because it wouldn't load my
galaxyIndices from the snaps.yaml in my default bucket.
I
?
In the mean time, I added more safeguards if this happens again:
https://github.com/galaxyproject/cloudman/commit/337ecb95a04788e540d60be37b4f4f817257b24f
On Tue, Jun 30, 2015 at 7:32 PM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi,
from IRC this question/bug report:
(18:06:13
Hi Enis,
I am trying to launch my cloudman instance with this launcher again:
https://launch.usegalaxy.org/launch
You created the flavor for me because it wouldn't load my
galaxyIndices from the snaps.yaml in my default bucket.
I thought, this problem was fixed, but it still creates a
At what galaxy version are you?
2015-06-30 7:36 GMT-05:00 Gildas Le Corguille lecorgui...@sb-roscoff.fr:
Hi,
We have a problem on our production instances since one or two years
(never found the time to write it and we still hope to find by ourself).
Some jobs stay in waiting status
2015-06-30 11:04 GMT-05:00 John Chilton jmchil...@gmail.com:
On Mon, Jun 29, 2015 at 2:48 PM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
I have a tool with filtered outputs (data [..]filter[...]/data).
A) As I understood the filters are pure python. But if I put
Hi,
from IRC this question/bug report:
(18:06:13) avowinkel: some cloudman guy here? enis?
(18:06:30) avowinkel: AttributeError: 'NoneType' object has no attribute
'id'
(18:06:50) avowinkel: when persisting galaxyIndices
(18:07:43) avowinkel: snapshot is created, but it crashes when ... somewhen
a
configuration issue.
-John
On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi Alexander,
I have opend an issue:
https://github.com/galaxyproject/planemo/issues/240
Thanks for reporting,
Bjoern
Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel:
Hi
Ay shit. Just realized during looking at it the third time:
Someone forgot to uncomment the key line o_o'
2015-06-29 16:21 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Here they are:
~/.planemo.yml: http://pastebin.com/nWdT6ybx
Command-Log: http://pastebin.com/baBmrD8d
2015
with and
send me a copy of that as well as the command-line that produced the
above output?
-John
On Mon, Jun 29, 2015 at 12:05 PM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Thanks,
now I get the following directly after the diff output:
Could not update stacks
object
Hi,
as many of you probably know by now,
I have a tool that creates an output collection
by discovering the datasets in this collection
like propsed there: [1]
Specifically I have a fastq input with set build
information (a ref genome).
The output is a collection of fastq files.
After I managed
FOR GOD'S SAKE SEARCH THE ARCHIVE !!!
http://dev.list.galaxyproject.org/Database-Build-td4140140.html
https://github.com/galaxyproject/tools-devteam/blob/master/tools/tophat2/tophat2_wrapper.xml#L313
2015-06-26 21:58 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi,
as many
And the corresponding pull request:
https://github.com/galaxyproject/tools-devteam/pull/173
The BWA github-repo is newer than what is on the toolshed, right? When do
you update the toolshed?
Best,
Alexander
2015-06-26 22:17 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
FOR GOD'S
Hi,
I'm running:
planemo shed_update --check_diff --shed_target toolshed
and get a python error message (see below).
shed_diff and shed_lint are working fine.
planemo, version 0.12.2
Best,
Alexander
Traceback (most recent call last):
File /usr/local/bin/planemo, line 11, in module
Hi Team,
my tool creates dynamically 96 datasets bundled into a list.
In the history I can see the number 96 in the top as hidden datasets
(6 shown, 96 hidden)
When I open the list, I just can see 64 items.
Now I run the job again and I have 96 more hidden items.
I open the new list and can see
metadata_source=fastq_input1), so perhaps
this is a bug - John?
Peter
P.S. Your help caption and output label both say FASTQ, but the
input also allows FASTA input. Typo?
On Thu, Jun 25, 2015 at 2:39 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi,
I have an input, that can
all files of the
form *.fq to *.${fastq_input1.ext}.
Hope this helps.
-John
On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
no - not a typo. The tool can process both.
It's just my naming, because I use it for fastq.
I'll change the help tag
(v3) - Bam(v3) - Bam,Bai(v3)
Best,
Alexander
[1]
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L314
2015-06-19 1:26 GMT-05:00 Björn Grüning bjoern.gruen...@gmail.com:
Hi Alexander,
Am 19.06.2015 um 01:44 schrieb Alexander Vowinkel:
Hi,
when I 'produce
, that already exist.
How could that be done?
Thanks,
Alexander
2015-06-18 18:44 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi,
when I 'produce' a bam file in my output, I can download the bam file and
a corresponding bai file.
I am now wondering where does the bai file come from
is still active, I guess.
2015-06-15 15:53 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi,
I have a custom tool_conf.xml in gbs_tools/gbs_tool_conf.xml
It is added to the config and loaded without problems.
toolbox tool_path=./gbs_tools
But when I want to install tools from
Hi,
I have the following problem:
First, the job scheduling didn't work.
I tried to upload a file, but the job was waiting.
Then I checked squeue, which timed out.
The slurm service was running.
Then I restarted the cluster.
Now I even have problems access the cloudman admin page.
Meaning, the
is that implemented?
Best,
Alexander
2015-06-15 10:17 GMT-05:00 John Chilton jmchil...@gmail.com:
On Wed, Jun 10, 2015 at 4:04 PM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi Folks,
thank you so far for the previous help. I got much further.
Now I'm stuck with data collections
Hi,
I have a custom tool_conf.xml in gbs_tools/gbs_tool_conf.xml
It is added to the config and loaded without problems.
toolbox tool_path=./gbs_tools
But when I want to install tools from a toolshed (test and main)
to it (Shed tool configuration file), it reports Error during
installation.
Hi,
the config/galaxy.ini is being overwritten when restarting Galaxy
via the CloudMan Console.
Unfortunately I can't find the file, that is used as template.
I searched on the whole machine for *.cloud, galaxy.ini* and
universe_wsgi.ini*. The only file I found was
Hi list-members,
I have a Cloud Man instance on amazon.
I did minimal adaption (installing some tools, adding an index)
I'm currently running only a master, which is allowed to run jobs.
I have now 3 jobs saying: This job is waiting to run
But in the CloudMan console it says:
Worker status:
.
It would be good to be able to see some information about a reason
why a job can not be executed and is waiting.
Is that somewhere implemented?
Best,
Alexander
2015-06-10 16:19 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com
:
Hi list-members,
I have a Cloud Man instance on amazon.
I did
this in!
Cheers,
Bjoern
Am 10.06.2015 um 00:10 schrieb Alexander Vowinkel:
Hi,
I would like to create a wrapper for a program.
For that I would like to test it, but I just found how to
create a tool in galaxy.
I couldn't find anything about how to create a
package as a dependency
Hi,
I would like to create a wrapper for a program.
For that I would like to test it, but I just found how to
create a tool in galaxy.
I couldn't find anything about how to create a
package as a dependency.
Can someone give me some help here?
Best,
Alexander
Hi,
I'd like to refer to an old post I found in the archive [1]
and ask if there has been some progress in this?
Best,
Alexander
[1]
http://dev.list.galaxyproject.org/Sending-tool-output-to-input-parameters-of-downstream-tool-s-tt4663398.html
Hi all,
I was recently wondering how it might
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