Re: [galaxy-dev] Change from Bitbucket to git
Thanks Marius, it does not look like it's working for me. There are to many changes in git diff... the git pull and cat local_changes.diff |patch -p1 -R gives me an endless list of differences. Cheers Jochen On 21.07.2015 11:41, Marius van den Beek wrote: Hi Jochen, I recently did this. Instructions are here: https://wiki.galaxyproject.org/Develop/SourceCode This has worked for me: (~/galaxy-dist is my production galaxy dir) cd ~ git clone https://github.com/galaxyproject/galaxy.git cd galaxy git reset --hard 3f1cec451f6dadee52a70a14fc6f6899f7aacdae cd ~/galaxy-dist hg 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 wrote: 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 subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Change from Bitbucket to git
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 subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] PLINK 1.90 wrapper
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 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mirDeep2 install error
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 such file or directory randfold.c: In function 'main': randfold.c:30: error: 'SQFILE' undeclared (first use in this function) randfold.c:30: error: (Each undeclared identifier is reported only once randfold.c:30: error: for each function it appears in.) randfold.c:30: error: 'sqfp' undeclared (first use in this function) randfold.c:38: error: 'SQINFO' undeclared (first use in this function) randfold.c:38: error: expected ';' before 'sqinfo' randfold.c:89: warning: incompatible implicit declaration of built-in function 'strcpy' randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this function) randfold.c:100: error: 'sqinfo' undeclared (first use in this function) randfold.c:103: warning: incompatible implicit declaration of built-in function 'malloc' randfold.c:103: warning: incompatible implicit declaration of built-in function 'strlen' randfold.c:136: warning: incompatible implicit declaration of built-in function 'fabs' randfold.c:158: warning: incompatible implicit declaration of built-in function 'free' make: *** [randfold] Error 1 Cheer Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mirDeep2 install error
Now it worked! I had to purge the old squid version 1.9g version because it still recognised the old one to be not correctly installed... Thanks Jochen On 22.03.2016 11:26, Bjoern Gruening wrote: > Can you remove and reinstall > > package_randfold_2_0 > > Hopefully this solves 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 >> 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 such file or directory >> randfold.c: In function 'main': >> randfold.c:30: error: 'SQFILE' undeclared (first use in this function) >> randfold.c:30: error: (Each undeclared identifier is reported only once >> randfold.c:30: error: for each function it appears in.) >> randfold.c:30: error: 'sqfp' undeclared (first use in this function) >> randfold.c:38: error: 'SQINFO' undeclared (first use in this function) >> randfold.c:38: error: expected ';' before 'sqinfo' >> randfold.c:89: warning: incompatible implicit declaration of built-in >> function 'strcpy' >> randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this >> function) >> randfold.c:100: error: 'sqinfo' undeclared (first use in this function) >> randfold.c:103: warning: incompatible implicit declaration of built-in >> function 'malloc' >> randfold.c:103: warning: incompatible implicit declaration of built-in >> function 'strlen' >> randfold.c:136: warning: incompatible implicit declaration of built-in >> function 'fabs' >> randfold.c:158: warning: incompatible implicit declaration of built-in >> function 'free' >> make: *** [randfold] Error 1 >> >> Cheer Jochen >> >> >> ___ >> 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 mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ > ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mirDeep2 install error
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, >> >> 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 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 mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ > ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] mirDeep2 install error
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 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Create a new datatype svg
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 your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create a new datatype svg
Hi Björn, thanks, so I just change the format to svg? or is there more to do? The output appears to be empty? Cheers Jochen On 07.02.2017 13:34, Björn Grüning wrote: > Hi Jochen, > > svg is supported, see here: > > https://github.com/galaxyproject/galaxy/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 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 your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> -- 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create a new datatype svg
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 correctly via > the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = True" > in galaxy.ini. Otherwise it will appear as plaintext xml. But do be aware of > the security concerns if you change this setting. Downloading/saving the svg > and then manually opening will work regardless. > > > Thanks for using Galaxy, > > Dan > ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create a new datatype svg
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 > ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] list of names, variables that cannot be used inside XML
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 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create a new datatype svg
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 one item in the history showing the png and if you click on save you have the option to also save svg. Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Update Galaxy from 15.10 to 16.10
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 ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Update Galaxy from 15.10 to 16.10
Thanks Jelle, now its running. I think matters where to put the conda statements inside the galaxy.ini. It does not work if you put them at the end of the file. Cheers Jochen On 17.01.2017 12:32, Jelle Scholtalbers wrote: > Hi Jochen, > > generally updating the database shouldn't be an issue as this is handled by > the migration scripts that incrementally update your db schema to match the > version. > But I would do a backup just in case. > > For the outdated ini files you can use the tool called Meld to spot > differences between yours and the .sample 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 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 >> ___ >> 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 mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > -- 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] apache on ubuntu
Hi Ray, yes exactly. So my problem is that I have no idea where to copy those settings. I have tutorial how it works on Centos but the file structure is different on Ubuntu. So I have my galaxy instance running on localhost:8080 (can also be moved to something else). If I run localhost or my local ip in a browser I see the apache also from a different PC in my network. So my idea is to redirect the apache or galaxy to my IP so that everyone in the network can see and use it (ssl encrypted if possible) Cheers Jochen On 02.09.2016 06:02, Raymond Wan wrote: Hi Jochen, I presume you looked at this already: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy Those instructions work for Ubuntu as well. What do your Apache2 error logs says (in /var/log/apache2/)? And what have you tried in your configuration files? And are you trying to forward port 80 to 8080, 443 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 local ip address. I read plenty of tutorials, can anyone help setting it up on Ubuntu? The files I have to modify are located at: /etc/apache2/sites-available/ 000-default.conf and default-ssl.config ? apache is up and running. Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] apache on ubuntu
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 are located at: /etc/apache2/sites-available/ 000-default.conf and default-ssl.config ? apache is up and running. Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] bug in fastqmcf
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 subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Docker on Windows 10
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 database. In addition I would like to install tools from the toolshed which will be kept after restarting the docker. So ware I did the following: docker run -d -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable its running but there are no files appearing at E:\galaxy_storage\ is it also possible to modify the galaxy.ini? or to ssh to the docker container? Thanks in advance Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Docker on Windows 10
In addition, this is the error message: *sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) could not connect to server: Connection refused* *Is the server running on host "localhost" (::1) and accepting* *TCP/IP connections on port 5432?* *could not connect to server: 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 and download galaxy-stable I can run it and tools can be installed including dataset are also not lost after shutdown. I haven't found the path for my files and I would like to modify also the galaxy.ini. The export path is set to c:/user/documents/kitematic/export but there are no files? On commandline (powershell) it is not possible to get it running. Somehow I get many errors like I told you before and the galaxy instance is never running in my browser. does anyone know where I can find the containers, I mean a path to my containers would be nice? If I run your commands on Linux its of curse working and I can set up everything that I need Cheers Jochen On 31.08.2016 16:08, Hans-Rudolf Hotz wrote: Hi Jochen I would definitively go for the native docker for Windows and not using docker tool box. Though, this is based on my experience using native docker for Mac versus docker tool box. Maybe someone else on the list has experience with running Bjoern's docker images on windows? Yes, once you get the '-v' option running, it will be possible to modify galaxy files and keep the changes. Hans-Rudolf 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 after closing the session? This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with startup > log 2>&1 & the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432? and its not running. and have access to the container. with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box? I'm using native docker for Windows. is there any benefit using docker tool box? Best Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Docker on Windows 10
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 will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with startup > log 2>&1 & the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432? and its not running. and have access to the container. with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box? I'm using native docker for Windows. is there any benefit using docker tool box? Best Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Docker on Windows 10
Hi Hans-Rudolf, here is my progress: If I use Kitematic and download galaxy-stable I can run it and tools can be installed including dataset are also not lost after shutdown. I haven't found the path for my files and I would like to modify also the galaxy.ini. The export path is set to c:/user/documents/kitematic/export but there are no files? On commandline (powershell) it is not possible to get it running. Somehow I get many errors like I told you before and the galaxy instance is never running in my browser. does anyone know where I can find the containers, I mean a path to my containers would be nice? If I run your commands on Linux its of curse working and I can set up everything that I need Cheers Jochen On 31.08.2016 16:08, Hans-Rudolf Hotz wrote: Hi Jochen I would definitively go for the native docker for Windows and not using docker tool box. Though, this is based on my experience using native docker for Mac versus docker tool box. Maybe someone else on the list has experience with running Bjoern's docker images on windows? Yes, once you get the '-v' option running, it will be possible to modify galaxy files and keep the changes. Hans-Rudolf 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 after closing the session? This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with startup > log 2>&1 & the startup takes quite a long time and also shows a lot of errors like: could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting tcp/ip connections on port 5432? and its not running. and have access to the container. with regard to using the '-v' option: are you using the native docker for Windows or are you using the docker tool box? I'm using native docker for Windows. is there any benefit using docker tool box? Best Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] apache on ubuntu
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 checked it from another PC inside the local network. I just saw the apache running. Changing the to the correct port did not give me access to my running galaxy. > I see you are editing the config file in /etc/apache2/sites-available; have > you enabled this site? That is, do you also see the config file in > /etc/apache2/sites-enabled? > I have to check again but I think I also saw the sides-enabled. Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] multiqc
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 and not on your production instance 15.10. Any suggestions? Thanks Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] apache on ubuntu
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 module you are using to achieve the above) >> has a logging facility, which you might want to read about: >> Yes I did a restart. Maybe I put the code to the wrong position? I think I will also ask somewhere else for help. Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Speedup Galaxy
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 people on this instance that should not be the problem. Does anyone have any idea? Disk-space? uptime of our server? big full database? ?? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] installing tool dependencies
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 "I installed a bunch of tools at the same time", > did you really trigger multiple installations at the same time, > or did you install a suite of tools? > I don't think the install framework can handle parallel installations > (well). > It may work once in a while, but you're better of installing things > sequentially. thats true. I guess that was the reason on all the errors. Thanks Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] installing tool dependencies
Hi, I installed a bunch of tools at the same time and ran into some errors. After repairing those tools some of the dependencies installations did not work. If I try to repair the tools again I also get this error message: Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. the tool I tried is called: Name: camera_annotate Description: [Metabolomics][W4M][LC-MS] CAMERA R Package - 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: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] wrapper for tool with multiple outputs
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 produce 3 files: /tmp/out_dup_log.txt /tmp/out.sorted.dedup.bam /tmp/out.sorted.markdup.bam so my question is if this out prefix will give me problems overwriting next output files coming from this tool? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] conda problem with R libraries
Hi all, I'm testing a tool with planemo and the conda dependencies are not running: r-base r-ggfortify r-getoptlong galaxy.jobs.handler INFO 2017-07-04 13:11:42,935 (2) Job dispatched galaxy.util.object_wrapper WARNING 2017-07-04 13:11:43,062 Unable to create dynamic subclass for , None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases ...The following specifications were found to be in conflict: - cairo 1.14.6 4 - r-assertthat (target=r-assertthat-0.1-r3.3.2_4.tar.bz2) -> r-base 3.3.2* ... ... somehow 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] primer blast tool
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 Zurich, Switzerland Phone +41 44 632 28 25 jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Firefox drag and drop not working
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 written like http://www.example.com/ Make sure that you’re using forward slashes (i.e. /). Is there anything to enable, install, or set inside Firefox? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] extract extra info (logs) from history
Hi Devon, do you mean Alignment Summary? How can I access that information and use it for an other tool. Cheers Jochen On 26.04.2018 14:14, Devon Ryan wrote: There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're 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 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 rate [bam_sort_core] merging from 21 f Is it possible to access these logs? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] extract extra info (logs) from history
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, or maybe Devon did already, where is the log info of HISAT saved? Cheers Jochen 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 Jochen On 26.04.2018 14:14, Devon Ryan wrote: There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're 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 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 rate [bam_sort_core] merging from 21 f Is it possible to access these logs? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] extract extra info (logs) from history
Thanks Devon, I think now I got it ;-). We are running 17.05 I might not have the "Summary Options" ? I cannot find them... But maybe I can use the flagstat tool for now. Cheers Jochen On 02.05.2018 16:34, Devon Ryan wrote: By default the logs are just to stdout. You need to use one of the options (under "Summary Options" on the version on our instance) if you want things saved as a history item. 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 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, or maybe Devon did already, where is the log info of HISAT saved? Cheers Jochen 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 Jochen On 26.04.2018 14:14, Devon Ryan wrote: There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're 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 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 rate [bam_sort_core] merging from 21 f Is it possible to access these logs? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] use or convert tool.xml file for database webpage
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 interpreted inside galaxy to generate the interface of a galaxy tool. thanks in advance Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] bigwig problem
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 ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] bigwig problem
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 > > And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage, > which still points to the old versions. I have an update here: > > https://github.com/galaxyproject/conda-iuc/pull/14 > > Once that is available you should be able to `conda update ucsc_tools` the > affected environments. I am also working on switching all of the > requirements so they depend on the individual ucsc-* packages from Bioconda > instead of the metapackage so we shouldn't need to maintain it in the > future. > > --nate ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] collections with more than 25,000 items
Thanks this helps a lot! Cheers Jochen On 30.08.2018 17:14, Peter Cock wrote: > There is a sweet spot for splitting your BLAST query fasta file > by sequence - one big file with 25000 sequences is not great, > but one sequence per file is the worst possible option. > > This is due to all the extra overheads, you would have 25000 > jobs submitted to the cluster, each of which would load the > BLAST binary and database off disk etc. And there are also > going to be Galaxy overheads with a large collection as well. > > I would suggest somewhere around 500 to 1000 gene sequences > per FASTQ query file is likely a safe choice. If you have very > long sequences (e.g. chromosomes or contigs), then use less. > > As to the number of threads for each BLAST job, more is better, > but what to pick will depend on your cluster and how often there > 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 jobs and run them >> only on one core... >> So my file has 25000 sequences and I'm blasting them against all NCBI >> proteins (nr). This just take to long time. I guess because the database >> is also very big? I tested this on the first 10 sequences and it took >> about 10mins. But maybe this is still not faster than running all at once? >> How many cores would you give such a job? >> >> Cheers Jochen >> >> On 30.08.2018 16:44, Peter Cock wrote: >>> If there are any limits, it would be down to the Galaxy Admin's job >>> settings - something generic with collections. >>> >>> Personally I've not done this - I tend to concatenate FASTA files >>> to make large files with multiple sequences instead. >>> >>> (And then we have the optional task splitting enabled so that Galaxy >>> breaks up the multiple-sequence FASTA file into chunks which >>> get shared out on our cluster for better throughput before >>> concatenating the output back into a single file.) >>> >>> Peter >>> On Thu, Aug 30, 2018 at 3:37 PM Jochen Bick >>> wrote: >>>> >>>> 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 >>>> >>>> -- >>>> 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.ch <mailto:jochen.b...@usys.ethz.ch> >>>> www.ap.ethz.ch >>>> ___ >>>> 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 mailing lists use the unified search at: >>>> http://galaxyproject.org/search/ >> >> -- >> 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.ch <mailto:jochen.b...@usys.ethz.ch> >> www.ap.ethz.ch -- 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] From Paste to uWSGI
t;> >> I think this is quite straightforward from the docs but again you need to >> tailor it for how you're handling job submission (e.g the "uwsgi + mules" >> doesn't need any handlers defining, but it looks like other strategies >> needs extra stuff defining here). >> >> -- Set up the proxying >> >> Assuming you're proxing via either Apache or nginx (we're using nginx), >> these are covered in the relevant sections: >> >> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html >> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html >> >> The main difference 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 previously. >> >> (There's also a "gotcha" if you're nginx configuration also tries to serve >> "static/scripts/packed", which needs to be removed - this is noted in the >> "breaking changes" for the 18.05 docs but is easy to miss.) >> >> Hopefully this is some help. There's lots of documentation, which is a >> good thing but which can sometimes make it harder to see where to start. >> >> Good luck with the update, >> >> Best wishes >> >> Peter >> >> -- >> Peter Briggs peter.bri...@manchester.ac.uk >> Bioinformatics Core Facility University of Manchester >> B.1083 Michael Smith Bldg Tel: (0161) 2751482 >> >> >> >> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf >> of Jochen Bick [jochen.b...@usys.ethz.ch] >> Sent: Monday, July 09, 2018 12:49 PM >> To: galaxy-dev@lists.galaxyproject.org >> Subject: [galaxy-dev] From Paste to uWSGI >> >> 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 Sciences >> Postal address: Universitätstrasse 2 >> <https://maps.google.com/?q=Universit%C3%A4tstrasse+2=gmail=g> >> / LFW B 58.1 >> 8092 Zurich, Switzerland >> Office: Eschikon 27 >> 8315 Lindau, Switzerland >> >> Phone +41 52 354 92 06 <+41%2052%20354%2092%2006> >> jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> >> www.ap.ethz.ch >> >> ___ >> 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 mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> ___ >> 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 mailing lists use the unified search at: >> http://galaxyproject.org/search/ > -- 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] From Paste to uWSGI
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 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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] bigwig problem
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
open shared object file: No such file or directory
Error outputting data
Error: Encountered internal Bowtie 2 exception (#1)
Command:
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/bowtie2-align-s
--wrapper basic-0 --local -k 2 --threads 5 -f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
(ERR): bowtie2-align exited with value 1
Error, cmd: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 5
-f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
| samtools view -@ 5 -F4 -Sb - | samtools sort -m 107374182 -@ 5 -no -
- >
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
2>tmp.54212.stderr died with ret 32512 at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/opt/trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1750
main::run_chrysalis("/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"..., 200, 500,
"RF", "/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...) called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1595
main::run_Trinity() called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1262
eval {...} called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1261
Trinity run failed. Must investigate error above.
has anyone got an idea?
Cheers Jochen
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[galaxy-dev] Ballgown does not work
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 ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Ballgown does not work
Hej Peter, thanks for the quick reply. My galaxy is a release_17.05 I think the xml is also broken. Cheers Jochen On 10.04.2018 15:28, Peter Cock wrote: > Are you trying to install this? > > https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b > > If so, it does set out its requirements: > > > version="2.2.0">bioconductor-ballgown > r-dplyr > r-optparse > > > However, your Galaxy would have to be using BioConda to do this. > This wrapper does not include a legacy 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 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 >> >> ___ >> 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 mailing lists use the unified search at: >> http://galaxyproject.org/search/ -- 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Ballgown does not work
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 you were trying to use in > Galaxy. Is it this version from Theo Collard: > > https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b > > If so, this appears to be where he develops it on GitHub, you > could file an issue there: and yes that is the version I'm trying to install. > > https://github.com/CollardT/Ballgown-Wrapper I can contact report the issue on github. It looks like its looking for a variable called dataset with is not defined in the input part. this looks like python code?: ## ## This function returns the name of the sample associated to a given file ## #def get_sample_name($dataset, $sample_mapping): ##If the file with samples mapping was provided #if $sample_mapping != None: #return $sample_mapping.get($dataset.name, None) ##Otherwise with extract the sample name from the filename #else: #return str($dataset.element_identifier) #end if #end def Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] bigwig problem
Hej Nate,
thanks, how to I install this on the galaxy specific conda? I have at
least 3 different conda version on my machine and also two galaxy
servers running. the last time i tried to update one of the packages
inside conda I broke the complete conda somehow...
Cheers Jochen
On 02.03.2018 17:49, Nate Coraor wrote:
This occurs when bzip2 is installed from defaults instead of
conda-forge. If you have Conda >= 4.0 this shouldn't happen as long as
you install with the right channel 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>> wrote:
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
open shared object file: No such file or directory
Error outputting data
Error: Encountered internal Bowtie 2 exception (#1)
Command:
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/bowtie2-align-s
--wrapper basic-0 --local -k 2 --threads 5 -f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
(ERR): bowtie2-align exited with value 1
Error, cmd: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 5
-f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
| samtools view -@ 5 -F4 -Sb - | samtools sort -m 107374182 -@ 5
-no -
- >
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
2>tmp.54212.stderr died with ret 32512 at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/opt/trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1750
main::run_chrysalis("/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
200, 500, "RF",
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...)
called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1595
main::run_Trinity() called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1262
eval {...} called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1261
Trinity run failed. Must investigate error above.
has anyone got an idea?
Cheers Jochen
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[galaxy-dev] tool output pattern syntax
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: sample_R1.cor.fq, sample_R2.cor.fq How can I catch the output? something like: library['lib'] == 'paired' but $input is the complete path ... Has anyone an idea? Cheer Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] bigwig problem
Hi,
I could solve the problem with bzip. Now this part is working.
Cheers Jochen
On 02.03.2018 17:49, Nate Coraor wrote:
This occurs when bzip2 is installed from defaults instead of
conda-forge. If you have Conda >= 4.0 this shouldn't happen as long as
you install with the right channel 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>> wrote:
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
open shared object file: No such file or directory
Error outputting data
Error: Encountered internal Bowtie 2 exception (#1)
Command:
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/bowtie2-align-s
--wrapper basic-0 --local -k 2 --threads 5 -f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
(ERR): bowtie2-align exited with value 1
Error, cmd: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 5
-f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
| samtools view -@ 5 -F4 -Sb - | samtools sort -m 107374182 -@ 5
-no -
- >
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
2>tmp.54212.stderr died with ret 32512 at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/opt/trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1750
main::run_chrysalis("/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
200, 500, "RF",
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
"/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...)
called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1595
main::run_Trinity() called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1262
eval {...} called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
line 1261
Trinity run failed. Must investigate error above.
has anyone got an idea?
Cheers Jochen
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[galaxy-dev] extract extra info (logs) from history
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 rate [bam_sort_core] merging from 21 f Is it possible to access these logs? Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Reinstall Galaxy by keeping database, database files and tools
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 ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] collections with more than 25,000 items
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 -- 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.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] installation is not finishing
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 are not getting installed. It looks like anything related to python is not getting installed? anyone needs some log file, please tell me. Cheers Jochen -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] installation is not finishing
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 are not getting installed. It looks like anything related to python is not getting installed? anyone needs some log file, please tell me. Cheers Jochen -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Update from 17.10 to 18.05
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: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:18:22 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:19 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:39 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from lstat, errno = 6 09/05/2018 11:57:40 ANS0361I DIAG: TransErrno: Unexpected error from GetFSInfo:stat, errno = 6 09/05/2018 11:57:40 ANS1999E Incremental processing of '/' stopped. Cheers Jochen ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Upload bigger 2GB
Hi, since some months we have the problem that users are allowed to upload files bigger 2GB. Is there some kind of options in the galaxy config that can stop this? Our data storage is not able to handle such big data duplication, we used to use Shared Data->Data libraries to reduce data duplication. Thanks in advance. Cheers Jochen -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: Upload bigger 2GB
Thanks, this might solve the problem indirectly. Jochen On 13.03.19 14:23, lecorguille wrote: quota per users -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Uncaught exception in exposed API method:
Hi,
I'm having this error since some minutes. The error message is coming in
the moment I click to any tool (e.g.: featurecounts) that provides data
collections. I think it has to do with a collection in my history. Here
some detail of my log file:
galaxy.web.framework.decorators ERROR 2019-02-06 15:50:09,026 Uncaught
exception in exposed API method:
Traceback (most recent call last):
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
line 113, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py", line
1903, in to_json
self.populate_model(request_context, self.inputs, state_inputs,
tool_model['inputs'])
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py", line
1951, in populate_model
tool_dict = input.to_dict(request_context)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 701, in to_dict
cond_dict["cases"] = list(map(nested_to_dict, self.cases))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 699, in nested_to_dict
return input.to_dict(trans)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 719, in to_dict
when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 717, in input_to_dict
return input.to_dict(trans)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
line 1966, in to_dict
match = dataset_collection_matcher.hdca_match(hdca)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/dataset_matcher.py",
line 226, in hdca_match
converted_ext, _ =
datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
formats)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/datatypes/registry.py",
line 892, 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 from datatype '%s'" %
(convert_ext, dataset.ext))
AttributeError: 'NoneType' object has no attribute 'ext'
82.130.95.243 - - [06/Feb/2019:15:50:08 +0200] "GET
/api/tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3%2Bgalaxy2/build?version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8_version=1.6.3%252Bgalaxy2
HTTP/1.1" 500 -
"http://green-l-bio.ethz.ch:8090/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2=1.6.3%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 data collections contains 8 fastq files.
Cheers Jochen
--
ETH Zurich
*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:jochen.b...@usys.ethz.ch>
www.ap.ethz.ch
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Re: [galaxy-dev] Uncaught exception in exposed API method:
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
in the moment I click to any tool (e.g.: featurecounts) that provides
data collections. I think it has to do with a collection in my
history. Here some detail of my log file:
galaxy.web.framework.decorators ERROR 2019-02-06 15:50:09,026 Uncaught
exception in exposed API method:
Traceback (most recent call last):
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
line 113, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1903, in to_json
self.populate_model(request_context, self.inputs, state_inputs,
tool_model['inputs'])
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1951, in populate_model
tool_dict = input.to_dict(request_context)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 701, in to_dict
cond_dict["cases"] = list(map(nested_to_dict, self.cases))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 699, in nested_to_dict
return input.to_dict(trans)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 719, in to_dict
when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 717, in input_to_dict
return input.to_dict(trans)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
line 1966, in to_dict
match = dataset_collection_matcher.hdca_match(hdca)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/dataset_matcher.py",
line 226, in hdca_match
converted_ext, _ =
datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
formats)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/datatypes/registry.py",
line 892, 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 from datatype '%s'" %
(convert_ext, dataset.ext))
AttributeError: 'NoneType' object has no attribute 'ext'
82.130.95.243 - - [06/Feb/2019:15:50:08 +0200] "GET
/api/tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3%2Bgalaxy2/build?version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8_version=1.6.3%252Bgalaxy2
HTTP/1.1" 500 -
"http://green-l-bio.ethz.ch:8090/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2=1.6.3%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 data collections contains 8 fastq files.
Cheers Jochen
--
ETH Zurich
*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:jochen.b...@usys.ethz.ch>
www.ap.ethz.ch
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Re: [galaxy-dev] Uncaught exception in exposed API method:
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 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
in the moment I click to any tool (e.g.: featurecounts) that provides
data collections. I think it has to do with a collection in my
history. Here some detail of my log file:
galaxy.web.framework.decorators ERROR 2019-02-06 15:50:09,026
Uncaught exception in exposed API method:
Traceback (most recent call last):
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
line 113, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1903, in to_json
self.populate_model(request_context, self.inputs, state_inputs,
tool_model['inputs'])
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1951, in populate_model
tool_dict = input.to_dict(request_context)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 701, in to_dict
cond_dict["cases"] = list(map(nested_to_dict, self.cases))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 699, in nested_to_dict
return input.to_dict(trans)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 719, in to_dict
when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 717, in input_to_dict
return input.to_dict(trans)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
line 1966, in to_dict
match = dataset_collection_matcher.hdca_match(hdca)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/dataset_matcher.py",
line 226, in hdca_match
converted_ext, _ =
datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
formats)
File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/datatypes/registry.py",
line 892, 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 from datatype '%s'" %
(convert_ext, dataset.ext))
AttributeError: 'NoneType' object has no attribute 'ext'
82.130.95.243 - - [06/Feb/2019:15:50:08 +0200] "GET
/api/tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3%2Bgalaxy2/build?version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8_version=1.6.3%252Bgalaxy2
HTTP/1.1" 500 -
"http://green-l-bio.ethz.ch:8090/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2=1.6.3%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 data collections contains 8 fastq files.
Cheers Jochen
--
ETH Zurich
*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:jochen.b...@usys.ethz.ch>
www.ap.ethz.ch
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[galaxy-dev] add labels to tools
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 -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] add labels to tools
Thanks Gildas, for the quick reply! That looks like the right page... but I don't see a concrete example. For example if I would like to add "new" to a tool? Cheers Jochen On 04.02.19 15:25, Gildas Le Corguillé wrote: Hi Jochen, Here is what you are looking for : https://galaxyproject.org/admin/tool-panel/#adding-labels-to-tools Cheers Gildas - Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff Sorbonne Université / CNRS Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 -- Le 4 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%2Fsauria%2Fhifive%2Fhifive%2F0.1.0>. How can I add these labels. Cheers Jochen -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/ -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] featureCounts with GFF
Hi, our group would like to switch to featureCounts <http://green-l-bio.ethz.ch:8090/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2> but we are using only GFF from NCBI. It looks like featureCounts <http://green-l-bio.ethz.ch:8090/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2> provides GFF but out of the box it does not provide a proper count table. The output looks like this: Status HISAT2 on data 33 Assigned5186527 Unassigned_Unmapped 518985 Unassigned_MappingQuality 1353602 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate0 Unassigned_MultiMapping 0 Unassigned_Secondary0 Unassigned_Nonjunction 0 Unassigned_NoFeatures 7515020 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity0 Geneid HISAT2 on data 33 5186527 I guess I need some advanced options? Which are different to the default run settings? Does anyone have a tutorial or example on how to configure the tool correctly with a standard GFF file, or does anyone also use GFF files? Or is there a better tool to use? Cheers Jochen -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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 mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] galaxy not running after galaxy.yml changes
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 at .venv
Traceback (most recent call last):
File "./scripts/manage_tool_dependencies.py", line 60, in
main()
File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in main
action_func(args, kwargs)
File "./scripts/manage_tool_dependencies.py", line 20, in _init_if_needed
_build_dependency_manager_no_config(kwargs)
File "./scripts/manage_tool_dependencies.py", line 48, in
_build_dependency_manager_no_config
dependency_manager = DependencyManager(**dependency_manager_kwds)
File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line 77,
in __init__
self.dependency_resolvers = self.__build_dependency_resolvers(conf_file)
File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line
241, in __build_dependency_resolvers
plugin_source = plugin_config.plugin_source_from_path(conf_file)
File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ", line 78,
in plugin_source_from_path
return ('xml', ElementTree.parse(path).getroot())
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse
tree.parse(source, parser)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse
parser.feed(data)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed
self._raiseerror(v)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
_raiseerror
raise err
xml.etree.ElementTree.ParseError: junk after document element: line 54,
column 0
Cheers Jochen
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[galaxy-dev] Re: galaxy-dev Digest, Vol 155, Issue 3
Thanks Matthias. Good to know. I thought we might confused the system by archiving a part of the data. Cheers Jochen Get BlueMail for Android On May 22, 2019, 08:42, at 08:42, Matthias Bernt wrote: >Dear Jochen, > >I don't know if its excpected. But at least I can tell that the same is > >happening here. And I can add if the 000 folder contains 000-999 the >pattern repeats in 001. > >Cheers, >Matthias > >On 21.05.19 17:38, galaxy-dev-requ...@lists.galaxyproject.org wrote: >> Coming back to my question: >> >> this is how an ls -ls looks in my database folder... >> >> 2. Apr 14:40 000/ >> 9. Nov 2015 005/ >> 19. Nov 2018 007/ >> 19. Nov 2018 008/ >> 3. Dez 2015 010/ >> 10. Jan 2017 012/ >> 10. Jan 2017 013/ >> 29. Jun 2017 014/ >> 4. Jul 2017 015/ >> 9. Jan 2018 018/ >> 29. Jun 2017 020/ >> 21. Sep 2016 021/ >> 20. Mär 2018 032/ >> 29. Jan 09:38 033/ >> 29. Jan 10:32 034/ >> 16. Jul 2018 035/ >> 30. Okt 2018 036/ >> 30. Okt 2018 037/ >> 30. Okt 2018 038/ >> 30. Okt 2018 039/ >> 29. Aug 2018 070/ >> 29. Aug 2018 071/ >> 29. Aug 2018 072/ >> 29. Aug 2018 073/ >> 29. Aug 2018 074/ >> 29. Aug 2018 075/ >> 29. Aug 2018 076/ >> 29. Aug 2018 077/ >> 29. Aug 2018 078/ >> 29. Aug 2018 079/ >> 29. Aug 2018 080/ >> 29. Aug 2018 081/ >> 29. Aug 2018 082/ >> 29. Aug 2018 083/ >> 29. Aug 2018 084/ >> 29. Aug 2018 085/ >> 29. Aug 2018 086/ >> 29. Aug 2018 087/ >> 29. Aug 2018 088/ >> 29. Aug 2018 089/ >> 29. Aug 2018 090/ >> 29. Aug 2018 091/ >> 29. Aug 2018 092/ >> 29. Aug 2018 093/ >> 29. Aug 2018 094/ >> 29. Aug 2018 095/ >> 31. Aug 2018 096/ >> 30. Aug 2018 097/ >> 1. Sep 2018 098/ >> 24. Okt 2018 099/ >> >> >> if you look into the 000 folder it restarts: >> >> 10. Dez 19:36 100/ >> 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 17:17 111/ >> >> 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 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 >>> >> -- ETH Zurich *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:jochen.b...@usys.ethz.ch> >> www.ap.ethz.ch > >-- > >--- >Matthias Bernt >Bioinformatics Service >Molekulare Systembiologie (MOLSYB) >Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ >Helmholtz Centre for Environmental Research GmbH - UFZ >Permoserstraße 15, 04318 Leipzig, Germany >Phone +49 341 235 482296, >m.be...@ufz.de, www.ufz.de > >Helmholtz-Zentrum für Umweltforschung GmbH - UFZ >Helmholtz Centre for Environmental Research GmbH - UFZ >Permoserstraße 15, 04318 Leipzig, Germany >Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) >max.musterm...@ufz.de, www.ufz.de > >Sitz der Gesellschaft/Registered Office: Leipzig >Registergericht/Registration Office: Amtsgericht Leipzig >Handelsregister Nr./Trade Register Nr.: B 4703 >Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: >MinDirig Wilfried Kraus >Wissenschaftlicher Geschäftsführer/Scientific Managing Director: >Prof. Dr. Georg Teutsch >Administrative Geschäftsführerin/Administrative Managing Director: >Dr. Sabine König ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: galaxy not running after galaxy.yml changes
Hej Nate,
thx for your email. We did not touch that file. Maybe we just have a
corrupted yml file? Is there a good way to check (lint) that file?
Cheers Jochen
On 09.05.19 19:56, Nate Coraor wrote:
> Hi Jochen,
>
> Could you check the value of the 'dependency_resolvers_config_file'
> 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 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 at .venv
> Traceback (most recent call last):
> File "./scripts/manage_tool_dependencies.py", line 60, in
> main()
> File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in
> main
> action_func(args, kwargs)
> File "./scripts/manage_tool_dependencies.py", line 20, in
> _init_if_needed
> _build_dependency_manager_no_config(kwargs)
> File "./scripts/manage_tool_dependencies.py", line 48, in
> _build_dependency_manager_no_config
> dependency_manager = DependencyManager(**dependency_manager_kwds)
> File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ",
> line 77,
> in __init__
> self.dependency_resolvers =
> self.__build_dependency_resolvers(conf_file)
> File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line
> 241, in __build_dependency_resolvers
> plugin_source = plugin_config.plugin_source_from_path(conf_file)
> File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ",
> line 78,
> in plugin_source_from_path
> return ('xml', ElementTree.parse(path).getroot())
> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182,
> in parse
> tree.parse(source, parser)
> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656,
> in parse
> parser.feed(data)
> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642,
> in feed
> self._raiseerror(v)
> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
> _raiseerror
> raise err
> xml.etree.ElementTree.ParseError: junk after document element:
> line 54,
> column 0
>
> Cheers Jochen
>
>
> ___
> 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:
> %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/
>
--
ETH Zurich
*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:jochen.b...@usys.ethz.ch>
www.ap.ethz.ch
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[galaxy-dev] Re: new datasets appear in database/files/000/
Coming back to my question: this is how an ls -ls looks in my database folder... 2. Apr 14:40 000/ 9. Nov 2015 005/ 19. Nov 2018 007/ 19. Nov 2018 008/ 3. Dez 2015 010/ 10. Jan 2017 012/ 10. Jan 2017 013/ 29. Jun 2017 014/ 4. Jul 2017 015/ 9. Jan 2018 018/ 29. Jun 2017 020/ 21. Sep 2016 021/ 20. Mär 2018 032/ 29. Jan 09:38 033/ 29. Jan 10:32 034/ 16. Jul 2018 035/ 30. Okt 2018 036/ 30. Okt 2018 037/ 30. Okt 2018 038/ 30. Okt 2018 039/ 29. Aug 2018 070/ 29. Aug 2018 071/ 29. Aug 2018 072/ 29. Aug 2018 073/ 29. Aug 2018 074/ 29. Aug 2018 075/ 29. Aug 2018 076/ 29. Aug 2018 077/ 29. Aug 2018 078/ 29. Aug 2018 079/ 29. Aug 2018 080/ 29. Aug 2018 081/ 29. Aug 2018 082/ 29. Aug 2018 083/ 29. Aug 2018 084/ 29. Aug 2018 085/ 29. Aug 2018 086/ 29. Aug 2018 087/ 29. Aug 2018 088/ 29. Aug 2018 089/ 29. Aug 2018 090/ 29. Aug 2018 091/ 29. Aug 2018 092/ 29. Aug 2018 093/ 29. Aug 2018 094/ 29. Aug 2018 095/ 31. Aug 2018 096/ 30. Aug 2018 097/ 1. Sep 2018 098/ 24. Okt 2018 099/ if you look into the 000 folder it restarts: 10. Dez 19:36 100/ 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 17:17 111/ 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 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 > -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] new datasets appear in database/files/000/
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 -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: conda not installing deps.
Hej Björn, We have activated all conda parameters in the yml. But when you install a tool the deps are not installed. So every tool is installed with no deps. Jochen Get BlueMail for Android On Jul 26, 2019, 21:07, at 21:07, "Björn Grüning" wrote: >Hi Jochen, > >what 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 >> >> #dependency_resolvers_config_file: >config/dependency_resolvers_conf.xml >> conda_prefix: /opt/galaxy/tools/_conda >> #conda_exec: null >> #conda_debug: false >> #conda_ensure_channels: 'iuc,conda-forge,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 >> >> >> >> >> -- >> ETH Zurich >> *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:jochen.b...@usys.ethz.ch> >> www.ap.ethz.ch >> >> ___ >> 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: >>%(web_page_url)s >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/ >> ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] trouble running the new galaxy instance
Hi since we updated some loc files our galaxy (19.01) does start but is unavailable in the browser. # systemctl status galaxy ? galaxy.service - SYSV: Galaxy http://galaxyproject.org/ Loaded: loaded (/etc/rc.d/init.d/galaxy; bad; vendor preset: disabled) Active: active (exited) since Mon 2019-07-15 10:23:11 CEST; 1 weeks 0 days ago Docs: man:systemd-sysv-generator(8) Process: 5840 ExecStop=/etc/rc.d/init.d/galaxy stop (code=exited, status=0/SUCCESS) Process: 5957 ExecStart=/etc/rc.d/init.d/galaxy start (code=exited, status=0/SUCCESS) Jul 15 10:23:11 green-galaxy galaxy[5957]: File "/opt/galaxy/galaxy/.venv/li...n Jul 15 10:23:11 green-galaxy galaxy[5957]: self.fetch_more_tokens() Jul 15 10:23:11 green-galaxy galaxy[5957]: File "/opt/galaxy/galaxy/.venv/li...s Jul 15 10:23:11 green-galaxy galaxy[5957]: return self.fetch_value() Jul 15 10:23:11 green-galaxy galaxy[5957]: File "/opt/galaxy/galaxy/.venv/li...e Jul 15 10:23:11 green-galaxy galaxy[5957]: self.get_mark()) Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError: mappin...e Jul 15 10:23:11 green-galaxy galaxy[5957]: in "/opt/galaxy/galaxy/config/gal...0 Jul 15 10:23:11 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 -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: trouble running the new galaxy instance
Thanks Marius for your quick reply, I will check the yml and send you the full report once I have feedback from my sysadmin. Cheer Jochen On 23.07.19 10:03, Marius van den Beek wrote: > Hi Jochen, > > can you post out the full logs ? > > Jul 15 10:23:11 green-galaxy 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, 23 Jul 2019 at 09:26, Jochen Bick <mailto:jochen.b...@usys.ethz.ch>> wrote: > > Hi > > since we updated some loc files our galaxy (19.01) does start but is > unavailable in the browser. > > # systemctl status galaxy > ? galaxy.service - SYSV: Galaxy http://galaxyproject.org/ > Loaded: loaded (/etc/rc.d/init.d/galaxy; bad; vendor preset: > disabled) > Active: active (exited) since Mon 2019-07-15 10:23:11 CEST; 1 > weeks 0 > days ago > Docs: man:systemd-sysv-generator(8) > Process: 5840 ExecStop=/etc/rc.d/init.d/galaxy stop (code=exited, > status=0/SUCCESS) > Process: 5957 ExecStart=/etc/rc.d/init.d/galaxy start (code=exited, > status=0/SUCCESS) > > Jul 15 10:23:11 green-galaxy galaxy[5957]: File > "/opt/galaxy/galaxy/.venv/li...n > Jul 15 10:23:11 green-galaxy galaxy[5957]: self.fetch_more_tokens() > Jul 15 10:23:11 green-galaxy galaxy[5957]: File > "/opt/galaxy/galaxy/.venv/li...s > Jul 15 10:23:11 green-galaxy galaxy[5957]: return self.fetch_value() > Jul 15 10:23:11 green-galaxy galaxy[5957]: File > "/opt/galaxy/galaxy/.venv/li...e > Jul 15 10:23:11 green-galaxy galaxy[5957]: self.get_mark()) > Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError: > mappin...e > Jul 15 10:23:11 green-galaxy galaxy[5957]: in > "/opt/galaxy/galaxy/config/gal...0 > Jul 15 10:23:11 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 > > -- > ETH Zurich > *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:jochen.b...@usys.ethz.ch> > <mailto:jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch>> > www.ap.ethz.ch <http://www.ap.ethz.ch> > > ___ > 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: > %(web_page_url)s > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] conda not installing deps.
Hi we have a new galaxy 19.01 instance and conda is somehow not running correctly: galaxy.yml #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml conda_prefix: /opt/galaxy/tools/_conda #conda_exec: null #conda_debug: false #conda_ensure_channels: 'iuc,conda-forge,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 -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: conda not installing deps.
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/dependency_resolvers_conf.xml > conda_prefix: /opt/galaxy/tools/_conda > #conda_exec: null > #conda_debug: false > #conda_ensure_channels: 'iuc,conda-forge,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 > > > > > -- > ETH Zurich > *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:jochen.b...@usys.ethz.ch> > www.ap.ethz.ch > > ___ > 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: > %(web_page_url)s > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ -- ETH Zurich *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:jochen.b...@usys.ethz.ch> www.ap.ethz.ch ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
