Re: [galaxy-dev] Change from Bitbucket to git

2015-07-21 Thread Jochen Bick
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

[galaxy-dev] Change from Bitbucket to git

2015-07-21 Thread Jochen Bick
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] Plot-bamstats

2015-10-16 Thread Jochen Bick
Hej Jose, according to this https://wiki.galaxyproject.org/Events/GCC2015?action=AttachFile=get=S6_T1_interactive-environments.pdf http://bam.iobio.io/ is coming soon for galaxy. Cheers Jochen On 16.10.2015 15:36, Jose Juan Almagro Armenteros wrote: > Hello, > > I have just installed the

[galaxy-dev] PLINK 1.90 wrapper

2016-05-30 Thread Jochen Bick
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

Re: [galaxy-dev] mirDeep2 install error

2016-03-22 Thread Jochen Bick
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

Re: [galaxy-dev] mirDeep2 install error

2016-03-22 Thread Jochen Bick
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

Re: [galaxy-dev] mirDeep2 install error

2016-03-22 Thread Jochen Bick
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, >> >

[galaxy-dev] mirDeep2 install error

2016-03-22 Thread Jochen Bick
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 ___ Please keep all replies on the list by

[galaxy-dev] Create a new datatype svg

2017-02-07 Thread Jochen Bick
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage

Re: [galaxy-dev] Create a new datatype svg

2017-02-07 Thread Jochen Bick
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

Re: [galaxy-dev] Create a new datatype svg

2017-02-07 Thread Jochen Bick
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

Re: [galaxy-dev] Create a new datatype svg

2017-02-07 Thread Jochen Bick
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 > ___

[galaxy-dev] list of names, variables that cannot be used inside XML

2017-02-20 Thread Jochen Bick
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 -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 5

Re: [galaxy-dev] list of names, variables that cannot be used inside XML

2017-02-20 Thread Jochen Bick
Ok ur right I cannot reproduce this error any more... must be a typo or I don't know, sorry guys. Cheers Jochen On 20.02.2017 14:44, John Chilton wrote: > Really, that doesn't sounds correct. Why is pmode not allowed? > > -John > > On Mon, Feb 20, 2017 at 5:22 AM, Jochen

Re: [galaxy-dev] Create a new datatype svg

2017-02-09 Thread Jochen Bick
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

[galaxy-dev] Update Galaxy from 15.10 to 16.10

2017-01-17 Thread Jochen Bick
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

Re: [galaxy-dev] Update Galaxy from 15.10 to 16.10

2017-01-17 Thread Jochen Bick
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

Re: [galaxy-dev] apache on ubuntu

2016-09-02 Thread Jochen Bick
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

[galaxy-dev] apache on ubuntu

2016-09-01 Thread Jochen Bick
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

[galaxy-dev] bug in fastqmcf

2016-09-01 Thread Jochen Bick
Hi they migrated the code of e-utils to github. Download path is corrupted: https://expressionanalysis.github.io/ea-utils/ Cheers Jochen ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your

[galaxy-dev] Docker on Windows 10

2016-08-30 Thread Jochen Bick
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

Re: [galaxy-dev] Docker on Windows 10

2016-08-31 Thread Jochen Bick
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

Re: [galaxy-dev] Docker on Windows 10

2016-08-31 Thread Jochen Bick
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

Re: [galaxy-dev] Docker on Windows 10

2016-08-31 Thread Jochen Bick
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

Re: [galaxy-dev] apache on ubuntu

2016-09-13 Thread Jochen Bick
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

[galaxy-dev] multiqc

2016-09-14 Thread Jochen Bick
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

Re: [galaxy-dev] apache on ubuntu

2016-09-13 Thread Jochen Bick
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

[galaxy-dev] Speedup Galaxy

2016-12-09 Thread Jochen Bick
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

Re: [galaxy-dev] Speedup Galaxy

2016-12-14 Thread Jochen Bick
Coraor wrote: > Hi Jochen, > > You might want to enable the heartbeat (see the relevant options in > galaxy.ini), so you can see what the threads are actually doing during that > period. This should give you some insight on the culprit. > > --nate > > On Mon, Dec 12, 2

Re: [galaxy-dev] Speedup Galaxy

2016-12-12 Thread Jochen Bick
Thanks for your reply but in my case it did not solve the problem... has anyone else good ideas to speed up galaxy? Cheers Jochen On 09.12.2016 17:07, Hendrickson, Curtis (Campus) wrote: > Jochen > > We once had a similar, sudden performance problem, and found that the setting > >

Re: [galaxy-dev] installing tool dependencies

2017-01-12 Thread Jochen Bick
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

[galaxy-dev] installing tool dependencies

2017-01-12 Thread Jochen Bick
- Annotation - Returns annotation results (isotope peaks, adducts and fragments) Maybe anyone has an idea how to solve this. Thanks in advance Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office

Re: [galaxy-dev] wrapper for tool with multiple outputs

2017-01-04 Thread Jochen Bick
Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Wed, Jan 4, 2017 at 1:18 PM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote: Thanks Devan, I just changed it! I have an other question. I used this to catch the output

[galaxy-dev] wrapper for tool with multiple outputs

2017-01-04 Thread Jochen Bick
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

[galaxy-dev] conda problem with R libraries

2017-07-04 Thread Jochen Bick
how the conflicts can not be resolved=? Cheers Jochen -- ETH Zurich *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

[galaxy-dev] primer blast tool

2017-10-13 Thread Jochen Bick
Hi all, has anyone yet worked on wrapping primer-blast? https://www.ncbi.nlm.nih.gov/tools/primer-blast/ Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092

[galaxy-dev] Firefox drag and drop not working

2017-08-25 Thread Jochen Bick
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