Hi David,
that is already possible with the current CloudMan release.
You can choose "Custom Instance Type" and put whatever
you like.
Best,
Alexander
2015-09-12 11:35 GMT-05:00 David Kovalic :
> Hi,
>
> I want to be able to use different AWS worker instance types than are
> currently provided
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
gt; --
> Jennifer Hillman-Jackson
> Galaxy Application Support
> http://usegalaxy.org
> http://galaxyproject.org
> http://biostar.usegalaxy.org
>
>
> On Tue, Sep 1, 2015 at 5:37 PM, Alexander Vowinkel <
> vowinkel.alexan...@gmail.com> wrote:
>
>> Hi,
>>
>> this pag
l 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 makes FileZilla break the connection.
&
Hi,
this page:
https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/ToolPanel
is linked here:
https://wiki.galaxyproject.org/Learn/AdvancedWorkflow
but does not exist.
How can I put my Workflow for all users into the Tool Panel?
Thanks,
Alexander
__
,
Alexander
2015-09-01 18:19 GMT-05:00 Alexander Vowinkel
:
> 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
>
> FileZilla Log: http://pastebin.
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
FileZilla Log: http://pastebin.com/zfACC6wH
ProFTP Log: http://pastebin.com/T9JxKVCb
With console FTP in linux I can connect, 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 2015-08
the failed jobs - this is not currently possible but
> really should be ideally.
>
> https://trello.com/c/lxVJy7fs
>
> -John
>
> On Mon, Jul 27, 2015 at 11:32 PM, Alexander Vowinkel
> wrote:
> > Hi,
> >
> > when I run a tool on a big collection with cloud
criticised 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
:
> Hi,
>
> can someone tell me something about this?
> Pointing at the runner stated in the log vs. expec
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
:
> Hi,
>
> I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml:
> I added a destination with fol
Hi,
when I run a tool on a big collection with cloudman,
I get the following error in at least one of the tasks:
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/drmaa.py", line
151, in queue_job
fh = file( ajs.job_file, "w" )
IOError: [Errno 11] Resou
Hi, can anyone can give a suggestion on this?
2015-07-17 16:50 GMT-05:00 Alexander Vowinkel
:
> Hi,
>
> I'm running cutadapt (from TS) on a collection with 96 datasets, started
> from a workflow as an intermediate step.
> About half of them fail with this message.
>
&
Hi,
I'm running cutadapt (from TS) on a collection with 96 datasets, started
from a workflow as an intermediate step.
About half of them fail with this message.
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py",
line 590, in finish_job
job_
Indeed, this would be the right approach.
But so far the current strategy is quite imputed also in tools.
E.g. BWA from devteam automatically sorts the bam afterwards - wanted or
not.
2015-07-17 11:59 GMT-05:00 Ryan G :
> I would think the correct approach would be to allow any bam file and if a
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
:
> Hi,
>
> I have this tool that creates a collection by discovery datasets.
> It always worked fine, but this time I had 3 Histories,
Hi,
I have this tool that creates a collection by discovery datasets.
It always worked fine, but this time I had 3 Histories, where I ran
the tool on three different datasets.
When it finished, the collections were empty.
The datasets, that should be in the collections however, were there.
Is tha
Problem seems to be that the RC3 AMI (ami-c1ad79aa) is not pulbic
2015-07-15 13:38 GMT-05:00 Alexander Vowinkel
:
> 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
> tha
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 t
ance now.
>
> On Mon, 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
>> InvalidParameterV
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 to get a volume that big for galaxy?
Best,
Alexander
___
Hi,
I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml:
I added a destination with following param:
-N1 --cpus-per-task 1
--mem-per-cpu=4G
Galaxy service was restarted after chaning this.
Now I get the error "Unable to run job due to a misconfiguration of the
Galaxy job running system. Ple
ou have more content from that log?
>
> 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.alex
s
>> under the impression I had fixed this. In the mean time, I updated your
>> flavor to specify snap-6f0b211d.
>>
>>
>>
>> On Wed, Jul 1, 2015 at 4:44 PM, Alexander Vowinkel <
>> vowinkel.alexan...@gmail.com> wrote:
>>
>>> Hi Enis,
&g
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 galaxyIndi
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
2015-06-30 11:04 GMT-05:00 John Chilton :
> On Mon, Jun 29, 2015 at 2:48 PM, Alexander Vowinkel
> wrote:
> > I have a tool with filtered outputs ([...]).
> >
> > A) As I understood the filters are pure python. But if I put it in
> > "
At what galaxy version are you?
2015-06-30 7:36 GMT-05:00 Gildas Le Corguille :
> 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 (grey) indefinitely.
>
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
:
> Here they are:
>
> ~/.planemo.yml: http://pastebin.com/nWdT6ybx
> Command-Log: http://pastebin.com/baBmrD8d
>
>
&g
> 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
> wrote:
> > Thanks,
> >
> > now I get the following directly after the diff output:
> >
> >>
Hi,
I have a tool with filtered outputs ([...]).
A) As I understood the filters are pure python. But if I put it in
"
ll get a better error message after the upgrade if there is still a
> configuration issue.
>
> -John
>
> On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning
> wrote:
> > Hi Alexander,
> >
> > I have opend an issue:
> > https://github.com/galaxyproject/planemo/issues/24
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
> sys
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
:
> FOR GOD'S SAKE SEARCH THE
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
:
> Hi,
>
> as many of you probab
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 t
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
t;
> But just use a shell command or something to rename 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
> wrote:
> > no - not a typo. The tool can process both.
> &g
also using 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
> wrote:
> > Hi
Hi,
I have an input, that can be fasta,fastqsanger,fastqillumina:
I have multiple outputfiles - bundled in a list collection:
The format_source parameter doesn't work - the files in the list (extension
fq) are of format "fq"
How can I make it possible that they are fasta,fastqsanger
id you run the image cleanup step? RabbitMQ's
> database needs to be cleaned up before building the image otherwise the
> application won't start properly and the AMQP connection will never be
> established.
>
> You can also post the entire CloudMan's log somewhere and I
Hi,
someone knows a cheat sheet with all the commands supported by cheetah?
Best,
Alexander
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, pleas
Bam(v2) -> Bam,Bai(v2) ->
Prog2 -> Bam,Bai(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 :
> Hi Alexander,
>
> Am 19.06.2015 um 01:44 schrieb
te the bai
files, that already exist.
How could that be done?
Thanks,
Alexander
2015-06-18 18:44 GMT-05:00 Alexander Vowinkel
:
> 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 doe
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?
When is it being generated, what code is used for that?
When I do multiple actions with my bam file - is the index generated every
time? (o
Hi,
in
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros,
macros are defined with
[...]
But when I look in IUC macros, I find the following:
[...]
Which one is the current standard?
Best,
Alexander
___
self.flush()
> File "/usr/lib/python2.7/socket.py", line 303, in flush
> self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
>
2015-06-16 13:59 GMT-05:00 Alexander Vowinkel
:
> Hi,
>
>
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
e question with the error message is still active, I guess.
2015-06-15 15:53 GMT-05:00 Alexander Vowinkel
:
> 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.
> ""
>
> But when I want to inst
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
"/mnt/cm/installed_files/
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.
""
But when I want to install tools from a toolshed (test and main)
to it ("Shed tool configuration file"), it reports Error during
installation.
Clicking on the tool, it says
he video. At what version is that implemented?
Best,
Alexander
2015-06-15 10:17 GMT-05:00 John Chilton :
> On Wed, Jun 10, 2015 at 4:04 PM, Alexander Vowinkel
> wrote:
> > Hi Folks,
> >
> > thank you so far for the previous help. I got much further.
> > Now I'
Hi list,
How can I delete multiple tools from my galaxy installation?
So far I just know how to uninstall single ones through "Manage installed
tool shed repositories" - But this is quite nasty if I want to uninstall
many of them.
Thanks,
Alexander
PS: I also posted this there: https://biostar.
ried it the 3rd time.
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
:
> Hi list-members,
>
> I have a Cloud Man instance on ama
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: I
Hi Folks,
thank you so far for the previous help. I got much further.
Now I'm stuck with data collections.
Because this is quite a list, I appreciate also answers to parts of my
questions ;)
I have two issues:
A) manual definition of data collections (any type) by user and/or admin
B) definition
ete example, we will help you to get
> 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
>
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'm trying to index some fasta files.
They are uploaded in data library and I also loaded them into
Data Manager history and my local history.
But when I open the Data Manager, I can't choose my file.
It says in "Source FASTA Sequence" only "No options available".
Can somebody help?
Best,
A
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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