update 17115
mv .hg .hg_backup
cp -R ~/galaxy/.git .
git pull (at this point I got a merge error!)
so I did:
git diff local_changes.diff
cat local_changes.diff |patch -p1 -R
git pull
git checkout release_15.05
Best,
Marius
On 21 July 2015 at 11:36, Jochen Bick jochen.b...@usys.ethz.ch
Hi,
is it possible to change from bitbucket to git? So I would like
future-update my galaxy from git instead from bitbucket.
Cheers Jochen
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Hi all,
I just found the plink tool in two version 1.9 and 1.7. It looks like
that it has no wrapper yet? Is it possible that the owner gives a
feedback about this? We are are very interested in that tool.
Cheers Jochen
___
Please keep all
Hej Björn,
so it did work in the development galaxy but not in our production
galaxy. Here I get the following error in package_randfold_2_0 after
successfully installing squid version 1.9g :
randfold.c:24:18: error: squid.h: No such file or directory
randfold.c:26:23: error: sre_random.h: No
es your problem,
> Cheers,
> Bjoern
>
>
> On 22.03.2016 11:21, Jochen Bick wrote:
>> Hej Björn,
>>
>> so it did work in the development galaxy but not in our production
>> galaxy. Here I get the following error in package_randfold_2_0 after
>> success
Thanks Björn, looks good!
Cheers Jochen
On 22.03.2016 10:46, Bjoern Gruening wrote:
> Hi Jochen,
>
> can you please try again I updated the recipes.
>
> Sorry for the inconvenience,
> Bjoern
>
> On 22.03.2016 10:24, Jochen Bick wrote:
>> Hi,
>>
>
Hi,
I tried to install suite_mirdeep_2_0. There is an error in the
dependencies of package_squid_1_9g the download link has change to
http://eddylab.org/software/squid/squid.tar.gz
Cheers Jochen
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Hi all,
I'm working on a tool that will have svg as an output file. Is this data
type already established? If not how do I start?
Cheers Jochen
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blob/dev/config/datatypes_conf.xml.sample#L282
>
> Cheers,
> Bjoern
>
> Am 07.02.2017 um 12:45 schrieb Jochen Bick:
>> Hi all,
>>
>> I'm working on a tool that will have svg as an output file. Is this data
>> type already e
Thanks Dan,
I would like to have it as plain text but no as a separate file in the
history but more like the solution of bam and bai files. Do you know how
to do that?
Cheers Jochen
On 07.02.2017 21:26, Daniel Blankenberg wrote:
> Just a quick note, if you want svg to be rendered as a graphics
Hej Björn,
ok you were right... I had a tool issue.
Now its working.
Cheers Jochen
On 07.02.2017 21:17, Björn Grüning wrote:
> Hi,
>
> just change it to svg. If the output is empty this could be a tool problem.
>
> Ciao,
> Bjoern
>
___
Hi all,
is there any list available of names that are not allowed to use inside
xml code? I just found out that "pmode" is one of them.
Cheers Jochen
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 5
Hi Dan,
I understand the option with this specific flag. What I mean is that for
example the file format bam has two file in one save button. So if you
click on save you can either save the bam file or the bai file. I would
liek to have the same feature with my png and svg. So that I have just
Hi,
today we tried to update from 15.10 to 16.10 which included an update of
your database from 129 to 131.
Do we necessary run into problem if we update from an one year old
instance? How is the galaxy.ini updated? Or galaxy.ini does not know any
conda yet.
Thanks in advance.
Cheers Jochen
ple files. Björn pointed me to this
> tool after opening this <https://github.com/galaxyproject/galaxy/pull/3410>
> PR.
>
> Cheers,
> Jelle
>
> On Tue, Jan 17, 2017 at 11:34 AM, Jochen Bick <jochen.b...@usys.ethz.ch>
> wrote:
>
>> Hi,
>>
>> today
to 8080 or something else?
Ray
On Fri, Sep 2, 2016 at 5:53 AM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
Hi,
I'm having trouble setting up the apache to redirect my local running galaxy
which runs on localhost:8080
I would like that people could have access inside the lab knowing my lo
Hi,
I'm having trouble setting up the apache to redirect my local running
galaxy which runs on localhost:8080
I would like that people could have access inside the lab knowing my
local ip address. I read plenty of tutorials, can anyone help setting it
up on Ubuntu? The files I have to modify
Hi
they migrated the code of e-utils to github. Download path is corrupted:
https://expressionanalysis.github.io/ea-utils/
Cheers Jochen
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Hi,
I am on the way to set up a Docker container on win 10. My problem is
that I do not often work on win 10. My idea is to set up a galaxy which
can be uses once in a while if needed and will be shutdown or not
started if not needed:
So I am interested in exporting all datasets including the
Connection refused*
*Is the server running on host "localhost" (127.0.0.1) and accepting*
*TCP/IP connections on port 5432?*
*Removing PID file /home/galaxy/logs/reports.pid*
Cheers Jochen
On 31.08.2016 16:22, Jochen Bick wrote:
Hi Hans-Rudolf,
here is my progress: If I use Kitematic
Hi Hans-Rudolf,
thanks for the quick reply.
docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/
bgruening/galaxy-stable /bin/bash
this looks really nice. Is it possible to modify galaxy files in the
interactive session or will it all be reseted after closing the session?
This
On 08/31/2016 01:56 PM, Jochen Bick wrote:
Hi Hans-Rudolf,
thanks for the quick reply.
docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/
bgruening/galaxy-stable /bin/bash
this looks really nice. Is it possible to modify galaxy files in the
interactive session or will it all be reseted
Hi Keith,
> You say you can see the Apache instance from other machines on the network. I
> assume you are accessing your machine via its local IP address (something
> like 192.168.1.x); what happens when you try to access Galaxy via
> http://192.168.1.x:8080?
>
Yes I used my local IP and
Hi,
I'm having trouble installing multiqc, this is the current error message:
Traceback (most recent call last):
File "setup.py", line 32, in
""".format(version))
ValueError: zero length field name in format
interestingly I could install it on our developer instance which runs on
16.01
Hi Will and Ray,
> You may need to load the mod_rewrite module. This can be done via:
> sudo a2enmod rewrite
I will try that. Is this also resetting the modules of apache?
>
> -Will
>
>>
>> I presume you've restarted the web server after making this change?
>>
>> Apache's mod_rewrite (the
We are running a Galaxy instance at our institute (version 15.10). Since
some month the speed/reaction time of the interface drastically
decrease. Sometimes there is a lack of more than a minute loading a
single tool. I restarted galaxy without any improvements. We are working
with up to 3
Hej Marius,
> what version of galaxy are you running?
we are running 15.10 but it will be updated next Monday.
> When you are doing this you should have a traceback in your logs,
> this would be helpful to understand what is going on.
ok I will check the logs for the error.
>
> When you say
- Annotation - Returns
annotation results (isotope peaks, adducts and fragments)
Maybe anyone has an idea how to solve this. Thanks in advance
Cheers Jochen
--
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
Office
Hi,
I have a tool that produces multiple output files a log file, two bam
files. (https://github.com/nugentechnologies/nudup)
The tool it self provides an option called --out to specify a path to a
directory with a prefix that will be added to the output files:
--out /tmp/out
this will
how the conflicts can not be resolved=?
Cheers Jochen
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
Office: Tannenstrasse 1 / TAN D 6.2
8092 Zurich, Switzerland
Phone +41 44 632 28 25
jochen.b...@usys.ethz
Hi all,
has anyone yet worked on wrapping primer-blast?
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Cheers Jochen
--
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
Office: Tannenstrasse 1 / TAN D 6.2
8092
Hi all,
we recently updated to our galaxy server and now we would like to use
the new feature drag and drop items from the history. It does not work
with Firefox but with chrome. In Firefox it says:
The address isn’t valid
The URL is not valid and cannot be loaded.
Web addresses are usually
under
"Summary Options".
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
Hi,
I w
On 02.05.2018 12:37, Langhorst, Brad wrote:
Flagstat might be a good choice here…
Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use it for
an other tool.
Cheers
many
On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
That's also an interesting tool. Which gives almost the same result as in
the log file of at HISAT output. I'm not sure why the number of mapped reads
are not 100% identical...
but anyway can someone tell me,
Hi,
I have a question regarding the layout of each tool. I would like to use
the same layout (same xml file) like inside galaxy to build a standalone
webpage for a database. Is it possible to convert or use the xml file
outside galaxy? My problem is that I have no idea how the xml file get
Hi,
how can I fix this problem?
bedGraphToBigWig: error while loading shared libraries: libmysqlclient.so.18:
cannot open shared object file: No such file or directory
I have the files in the local bin but somehow it does not work inside galaxy.
Thanks in advance.
Cheers
Jochen
Thanks, nate,
can you tell me one I can update? And what i need to update?
Cheers Jochen
On 15.02.2018 16:24, Nate Coraor wrote:
> Hi Jochen,
>
> I ran in to this yesterday, we're working on fixing it right now. It's due
> to this:
>
> https://github.com/bioconda/bioconda-recipes/issues/5430
> are threads free on nodes. I would suggest trying 4, 8 or 16 threads.
>
> I hope that helps.
>
> Peter
>
>
> On Thu, Aug 30, 2018 at 3:50 PM Jochen Bick wrote:
>>
>> Thanks Peter,
>>
>> so my idea was to split my problem into single blast job
I noticed for nginx is that you no longer need to use
>> the "upstream"/"proxy_pass" directives, as nginx can talk directly to uwsgi
>> using a "uwsgi_pass" directive that connects to the socket defined in the
>> "uwsgi" section of galaxy.yml previousl
Hi all,
we would like to update to 18.05 and thereby also update our Paste Server.
https://docs.galaxyproject.org/en/latest/admin/scaling.html
Is there any tutorial on how to update from Paste to uWSGI?
Cheers Jochen
--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural
Hej all,
I'm also facing another problem which might be related to my previous
error, when I run Trinity:
samtools: error while loading shared libraries: libbz2.so.1.0: cannot
open shared object file: No such file or directory
samtools: error while loading shared libraries: libbz2.so.1.0: cannot
Hi,
I'm trying to install Ballgown but it throws some error message after
running it:
cannot find 'dataset' while searching for 'param_name.dataset.dataset'
the script does not have test-data file and it also does not install the
requirements.
Cheers Jochen
y Galaxy XML file to declare
> its package dependencies.
>
> What version of Galaxy do you have?
>
> Peter
>
> On Tue, Apr 10, 2018 at 2:16 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote:
>> Hi,
>>
>> I'm trying to install Ballgo
Hi Peter,
> "The short answer is that as of 17.01, Galaxy should install Conda
> the first time it starts up and be configured to use it by default."
yes, it installs everything with conda. So that should work, but I could
also set it up my self manually.
> You didn't confirm which Ballgown
one with:
conda install -n __trinity@2.4.0 -c conda-forge bzip2=1.0.6=1
--nate
On Thu, Mar 1, 2018 at 10:41 AM, Jochen Bick <jochen.b...@usys.ethz.ch
<mailto:jochen.b...@usys.ethz.ch>> wrote:
Hej all,
I'm also facing another problem which might be related to my previous
Hi,
I have a problem with the output of rcorrector which I would like to
wrap. The input are single-end or paired-end fastq file/s and the output
is the name (name of the input file) of the files plus ".cor.fq" so for
example:
input: sample_R1.fastq, sample_R2.fastq
output:
nel order e.g. `-c iuc -c bioconda -c
conda-forge -c defaults`. You should be able to fix this one with:
conda install -n __trinity@2.4.0 -c conda-forge bzip2=1.0.6=1
--nate
On Thu, Mar 1, 2018 at 10:41 AM, Jochen Bick <jochen.b...@usys.ethz.ch
<mailto:jochen.b...@usys.ethz.ch>> w
Hi,
I would like to use the info (log) HISAT is showing, for another tool.
e.g.:
26781724 reads; of these:
26781724 (100.00%) were unpaired; of these:
2445411 (9.13%) aligned 0 times
20399099 (76.17%) aligned exactly 1 time
3937214 (14.70%) aligned >1 times
90.87% overall alignment
Hi,
is it possible to clone a fresh galaxy and reinstall all tools from an
existing galaxy (old) by keeping the database and all files?
Cheers Jochen
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Hi,
is there any limit to run BLAST jobs from a collection of single FASTA
files? I started a job but is does not get executed... its just sending
for about an hour.
Cheers Jochen
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address
It's fixed a restart and uninstall of the half installed tool helped.
Cheers Jochen
On 23.11.18 09:32, Jochen Bick wrote:
Hi,
I wanted to install two tools but my installation is stuck in
Installing tool dependencies. So I found out that the xmls are cloned
but the dependencies
me.
Cheers Jochen
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland
Phone +41 52 354 92 06
jochen.b...@usys.ethz.ch <mailto:joche
Hi,
today we tried to update from 17.10 to 18.05
your server is running but with out any interface, its just white after
loading?
Galaxy
| AP - Group
# tail ./galaxy-dist/dsmerror.log
09/05/2018 11:18:21 ANS0361I DIAG: TransErrno:
ata
duplication.
Thanks in advance.
Cheers Jochen
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland
Phone +41 52 354 92 06
jochen.b...@usys.ethz
Thanks, this might solve the problem indirectly.
Jochen
On 13.03.19 14:23, lecorguille wrote:
quota per users
--
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315
6.3%2Bgalaxy2&__identifer=ku6ydfn1c8;
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/72.0.3626.81 Safari/537.36"
Any ideas? Errors only occur if I'm in that history. I can also provide
more information. This is running on a Galaxy 18.09.
The da
UPDATE:
I think it is the combination of data collection and Bam files in a data
collection. If I delete the HISAT result the error is gone. Any idea?
Cheers Jochen
On 06.02.19 16:02, Jochen Bick wrote:
Hi,
I'm having this error since some minutes. The error message is coming
I found the solution:
http://dev.list.galaxyproject.org/regarding-galaxy-kickstart-td4671625.html
we were running an old datatypes_conf.xml
I guess it was not updated when we updated galaxy.
Cheers Jochen
On 06.02.19 18:45, Jochen Bick wrote:
UPDATE:
I think it is the combination of data
Hi,
I'm interested to add labels to tool such as shown on usegalaxy.org for
example for the tool hifive
<https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsauria%2Fhifive%2Fhifive%2F0.1.0>.
How can I add these labels.
Cheers Jochen
--
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*Joche
févr. 2019 à 15:20, Jochen Bick <mailto:jochen.b...@usys.ethz.ch>> a écrit :
Hi,
I'm interested to add labels to tool such as shown on usegalaxy.org
<http://usegalaxy.org> for example for the tool hifive
<https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%
better tool to use?
Cheers Jochen
--
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland
Phone +41 52 354 92 06
jochen.b...@usys.ethz.ch <
Hi all,
we are testing a newly cloned galaxy. Which was running as expected a
few hours ago. After some modification to galaxy.yml file we got this
error message but after using the original galaxy.yml version it still
does not run.
Regenerating static plugin directories.
Activating virtualenv
00/
>> 30. Nov 10:45 101/
>> 10. Dez 19:39 102/
>> 10. Dez 19:37 103/
>> 11. Jan 15:13 104/
>> 11. Jan 11:31 105/
>> 22. Jan 14:33 106/
>> 8. Feb 10:46 107/
>> 14. Feb 15:47 108/
>> 21. Mär 11:00 109/
>> 2. Apr 15:22 110/
>> 21. Mai 17:
> option and verify that the file it points at (by
> default, config/dependency_resolvers_conf.xml) is properly formatted?
>
> --nate
>
> On Thu, May 9, 2019 at 1:25 PM Jochen Bick <mailto:jochen.b...@usys.ethz.ch>> wrote:
>
> Hi all,
>
> we are
/
21. Mär 11:00 109/
2. Apr 15:22 110/
21. Mai 17:17 111/
is this the expected behavior?
The only thing we did was we archived some of the very early generated
datasets. Is this maybe the problem?
Cheers Jochen
On 14.05.19 15:32, Jochen Bick wrote:
> Hi,
>
> today we found out that so
Hi,
today we found out that some of our files in your galaxy instance are
new in "database/files/000/" which is the first folder of your database
files. Could some please explain me how galaxy generates new file names?
and how this is possible?
Thanks in advance Jochen
--
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is not working? Do you have any error message.
>
>Ciao,
>Bjoern
>
>Am 25.07.19 um 15:45 schrieb Jochen Bick:
>> Hi
>>
>> we have a new galaxy 19.01 instance and conda is somehow not running
>> correctly:
>>
>> galaxy.yml
>>
&g
green-galaxy galaxy[5957]: ...done.
Jul 15 10:23:11 green-galaxy systemd[1]: Started SYSV: Galaxy
http://galaxyp
Hint: Some lines were ellipsized, use -l to show in full.
Has anyone a good hint?
Cheers Jochen
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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sci
axy galaxy[5957]: yaml.scanner.ScannerError:
> mappin...e
> Jul 15 10:23:11 green-galaxy galaxy[5957]: in
> "/opt/galaxy/galaxy/config/gal...0
>
> probably means that you have syntax error in galaxy.yml, but the full
> logs will tell you more.
>
> Best,
> Marius
>
> On Tue
,bioconda,defaults'
#conda_use_local: false
conda_auto_install: true
conda_auto_init: true
conda_copy_dependencies: true
job_working_directory: /opt/galaxy/daten/jobs_directory
any ideas?
Thanks Jochen
--
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*Jochen Bick*
Animal Physiology
Institute of Agricultural
are there any special setting needed for the _conda folder 755 ist ok?
On 25.07.19 15:45, Jochen Bick wrote:
> Hi
>
> we have a new galaxy 19.01 instance and conda is somehow not running
> correctly:
>
> galaxy.yml
>
> #dependency_resolvers_config_file: config/depen
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