ure how this can be Galaxy
> related.
>
> Is this still a problem?
>
> Cheers,
> Bjoern
>
> Am 08.03.19 um 09:23 schrieb Previti:
>> Dear Galaxy Community,
>>
>> I just recently started testing the Bismark methylation tools,
>> everything works
makes Galaxy run faster.
> but it actually just increases the amount of concurrent requests
> Galaxy can handle.
>
> Best,
> Marius
>
> On Wed, 10 Jul 2019 at 11:43, Previti
> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>
> Dear all,
>
&g
22f6f70742f67616c6178792f736865645f746f6f6c73222c20227265706f5f696e666f5f6469637473223a2...
0x7f9f35cdfed0>)
webob._parsed_query_vars: (GET([]), '')
webob.is_body_seekable: True
wsgi process: 'Multithreaded'
wsgi.input_terminated: True
--
*Dr. Christopher Previti*
Genomics and Proteomics C
, error was:file has no sequences defined
(mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False//
/
When I try to visualize it.
I hope I helped somebody with these infos.
Christopher
On 3/15/19 4:43 PM, Previti wrote:
> Dear all,
>
> I'm having serious issues with picard
ion.so
from
jar:file:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__picard@2.18.2/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
does anybody know what's going on?
The output "bam" file is the correct size (>20GB) but not readable...
Thanks and b
ot;FlyBase"; gene_biotype "pseudogene";
I'm assuming this is the "standard" GTF format (according to ensembl)
How's the best way to make this type of thing known...?
Cheers,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput
I got it, sorry to bother you.
One can actually specify the type of collection...and set it to list of
dataset pairs.
Best regards,
Christopher
Am 24.01.19 um 10:19 schrieb Christopher Previti:
Dear Galaxy Community,
Is there a way to input a paired dataset collection into a workflow?
I
Dear Galaxy Community,
Is there a way to input a paired dataset collection into a workflow?
I would like to build a workflow using cutadapt with a paired dataset
collection but...I'm missing something.
I have seen workflows (at usegalaxy.eu for example:
; Cheers,
> Nicola
>
> On 03/12/2018 13:33, Previti wrote:
>> Dear all,
>>
>> In my ongoing saga concerning our data libraries, I came across
>> another issue after our update from 17.09 to 18.05.
>> When trying to import fastq.gz files into a data library
the data type to fastq.gz in order for it to
work at all and even then it sometimes ends up throwing an error (state
= error).
Is there anything in particular I need to change to make this work reliably?
Cheers,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
Dear all,
I got it to work again.
I just added:
user_library_import_symlink_whitelist = "/symlink_target_folder"/
to the galaxy.ini (we'll switch to the .yml next update).
It got recognized and the symlinks can be used again.
Best regards,
Christopher
On 11/28/18 9:25 AM, Pre
berg.de <mailto:gal...@ad.dkfz-heidelberg.de>)
>
> Youssef Ghorbal
> IIS / DSI
> Institut Pasteur
> -
>> On 27 Nov 2018, at 11:43, Previti
>> > <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>>
>> Dear Youssef
work anymore in v18.05?
Is it a galaxy.ini configuration issue?
Thanks for any advise you could provide!
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under
. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661
christopher.prev
Ok thanks!
On 10/23/2018 11:14 AM, Marius van den Beek wrote:
> Dear Christopher,
>
> You need to copy the shipped datatypes_conf.xml.sample to the
> appropriate location(s) for your installation.
>
> Best,
> Marius
>
>
> On Tue, Oct 23, 2018, 11:08 AM Previti
>
r_dataset_by_extensions(extension,
formats)
File "/opt/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 891,
in find_conversion_destination_for_dataset_by_extensions
self.log.warning("Datatype class not found for extension '%s', which
is used as target for conversion
on_destination_for_dataset_by_extensions(extension,
formats)
File "/opt/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 891,
in find_conversion_destination_for_dataset_by_extensions
self.log.warning("Datatype class not found for extension '%s', which
is used as target for conve
hen re-install deseq2.
Once you update to a newer Galaxy version you can comment the
conda_ensure_channels setting again
and continue using the default channel order that Galaxy ships.
Hope that helps,
Marius
On Tue, 18 Sep 2018 at 12:18, Christopher Previti
mailto:christopher.prev...@dkfz-heidelb
-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6:
undefined symbol: PC
Does anybody know what to do about this?
Thanks and best regards,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing
-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6:
undefined symbol: PC
Does anybody know what to do about this?
Thanks and best regards,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing
t; questions some time ago...
>
>
>
> *From: *"Björn Grüning"
> *To: *"Previti" ,
> "galaxy-dev"
> *Sent: *Friday, September 7, 2018 9:56:41 AM
>
> 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, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy
to the newest Galaxy version is not
possible for us at the moment.
Any tips on how I could do this?
Thanks and best regards,
Christopher Previti
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ
s and best regards,
Christopher Previti
<http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/monitor_repository_installation?installing_repository_ids=17912123b7aa6af3,c2f15bb285119094,4a31abf1f877a79d,b1208393f3608833,d796ca8e1687a54b,53fb5c5113d9beb7,6df0b7b066ddc4c9,9c1
users with the same email address, unless you've changed that -- can
> you elaborate on what you've done?
>
> -Dannon
>
> On Wed, May 16, 2018 at 9:48 AM Previti
> <christopher.prev...@dkfz-heidelberg.de
> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
not able to reproduce
> it on my local instance. Can you provide a screenshot of what you're
> seeing, and the organization of the histories that are being sourced
> for the incorrect datasets?
>
> On Wed, May 16, 2018 at 7:25 AM Previti
> <christopher.prev...@dkfz-heidelbe
g?
Thanks and best regards,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/
larly check the total size of the working
>> directories and do the clean up manually
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>>
>> On 04/27/2018 01:51 PM, Previti wrote:
>>> Hi everybody,
>>>
>>> I have a hopefully basic questions re
do this regularly?
Would a quota prevent something like this from happening again or would
the jobs have to finish before being "counted"?
Thanks and best regards,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformat
s and best regards,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +
the website owners to inform them of this problem.
Any idea how to solve this...? This is the first time I'm seeing itI
tried changing the data type multiple times (fastq, fastq.gz,
fastqsanger...etc) but this doesn't get rid of it.
Best regards,
Christopher Previti
--
*Dr. Christopher
Dear all,
Does anybody know how to configure galaxy to actually show errors under
the "show tool errors" section of the admin interface?
I can't find any infos about this...we're running version 17.05.
Thanks and best regards,
Christopher
--
*Dr. Christopher Previti*
Genomics and
but still not
ideal.
I have about 10 histories that I cycle through on a regular basis.
Doesn't the system support that many?
Cheers,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
.*
Change
Line 63: tmp_file = tempfile.NamedTemporaryFile( 'w+b' )
to
tmp_file = tempfile.NamedTemporaryFile( 'w+' )
Then it'll work.
Cheers,
Christopher
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research
>
> Am 06.07.2017 um 13:05 schrieb Previti:
>> Dear all,
>> I seemly have a java issue (out of memory) when trying to construct a
>> picard index for the rat (rn6) genome build using the
>> picard_index_builder_data_manager.
>> This is strange because other, bigger
It worked, thanks again!
On 07/05/2017 03:37 PM, Previti wrote:
>
> Thanks, I'll give it a try!
>
> Cheers,
>
> Christopher
>
>
> On 07/05/2017 03:13 PM, Ignacio EGUINOA wrote:
>> Hi
>>
>> I had the same problem with deeptools, I guess the orig
t so that you can solve it in the meantime while we wait for
> someone to explain what can be wrong with the bzip2 package.
>
> cheers,
> Ignacio
>
> ----
>
> *From: *"Previti" <christopher.
Thanks a lot, it works now!
Am 17.01.2017 um 16:45 schrieb Nate Coraor:
Hi Christopher,
It's been up for a while now. The IP address is now 128.118.250.24 -
is it still resolving to 128.118.250.10 for you?
--nate
On Mon, Jan 16, 2017 at 3:01 AM, Christopher Previti
<christopher.p
(128.118.250.10):
Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(128)
[Receiver=3.1.1]
My colleague Georgios Nikolis and I are working on a local Galaxy
installation at the DKFZ and would really like to use the pre-built indices.
Cheers,
Christopher Previti
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