[galaxy-dev] Error in sh manage_db.sh -c ./config/galaxy.ini upgrade

Dear Galaxy Dev Team, We upgraded our Galaxy instance to the git repository from mercurial old Galaxy-dist to Galaxy. When running the sh manage_db.sh -c ./config/galaxy.ini upgrade we get the following error. Can you explain this error and more importantly how to correct the problem> Th

Re: [galaxy-dev] Galaxy Startup Failing

Hi Keith, I use start-stop-daemon to launch python and I pass --chuid and --group to start-stop-daemon so that galaxy does not run as root. It is my understanding that start-stop-daemon creates the pid file as root before changing user, as my /var/run/galaxy.pid is owned by root:root. I have attac

Re: [galaxy-dev] R: Re: FASTQ Groomer tool

Thank you so much guys! I appreciate your help immensely! On Nov 5, 2015 7:12 PM, Nicola Soranzo wrote: Hi Edgar, to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler pr

[galaxy-dev] R: Re: FASTQ Groomer tool

Hi Edgar, to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler processes will know about it only after a restart. Cheers, Nicola Martin Čech ha scritto >Hi

[galaxy-dev] Galaxy Url for Fasta and Bed index files

Hello, What is an appropriate galaxy URL to use to obtain bed and fasta index files? I have tried below: myGalaxy.org:port/dataset/get_metadata_file?hda_id=[fasta_dataset_id]&metadata_name=fasta.fai {for fasta index} and myGalaxy.org:port/dataset/get_metadata_file?hda_id=[bed_dataset_id]&metada

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart. I updated the wiki ( https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutor

Re: [galaxy-dev] FASTQ Groomer tool

Hello Nicola and Martin, The service galaxy restart worked. Can you guys give me a small explanation please? Just for my understanding… Cordialement / Regards, Edgar Fernandez De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola Soranzo Envoyé : November-05-15 2:33 PM À :

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, it seems you are hitting this fail: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#L124 which hints that the tool is not properly loaded in the toolbox. Did you restart the server and handlers after you installed the tool? I cannot help with the MySQL as we d

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, you can try to restart Galaxy (both web and handler processes) and re-run the tool. Cheers, Nicola On 05/11/15 19:18, Fernandez Edgar wrote: Hello again, I installed today the tool : fastq_all_to_sanger I get the same SQL error with that one too. Any ideas guys? Thank you!!! C

Re: [galaxy-dev] FASTQ Groomer tool

Hello again, I installed today the tool : fastq_all_to_sanger I get the same SQL error with that one too. Any ideas guys? Thank you!!! Cordialement / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : November-04-15 8:58 AM À : 'galaxy-...@bx.psu.edu' Objet : [galaxy-dev] FASTQ Groomer tool

Re: [galaxy-dev] login problem (redirection to the login page)

Hello, I've been struggling with the login issue with Galaxy for a while now. Try to use "incognito mode" on your browser when accessing the url for Galaxy and see what happens. Also if you don't really need for your users to activate their accounts by e-mail set the "user_activation_on=False"

Re: [galaxy-dev] login problem (redirection to the login page)

Hi, I come back to you with some news of my login problem. I delete my browser cache and cookies with no result. I restart all my services (Apache, PostgreSQL, Galaxy) with no more result. I try to start fresh with my PostgreSQL database cluster (to clear all the user information). But it didn't s

Re: [galaxy-dev] OpenMS caused Error downloading from URL

Hi Mic and Olivier, if there is broader interest in OpenMS please let me know. We have new wrappers and new installation instructions here: https://github.com/bgruening/galaxytools/tree/master/tools/openms + pre-compiled binaries as this takes ages to compile. Cheers, Bjoern Am 05.11.2015 um 15

Re: [galaxy-dev] OpenMS caused Error downloading from URL

Hello Mic, You should try to change the link in the tool_dependencies.xml of openMS with this link : http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10.0.tar.gz/ and t

[galaxy-dev] OpenMS caused Error downloading from URL

Hello I tried to install OpenMS ( toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms), but I have got the following error: File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.install

Re: [galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

Nicola, thanks a bunch! Your eyes are phenomenal! Greg > On Nov 4, 2015, at 8:09 PM, Nicola Soranzo wrote: > > Hi Greg, > in the inputs the param has name "input_gff", while in the test you are using > name "input". > > Cheers, > Nicola > > Von Kuster, Greg ha scritto > >> Hell

[galaxy-dev] package_xz_5_0_5 - Error downloading from URL:

Hello, package_xz_5_0_5 ( toolshed.g2.bx.psu.edu/repos/iuc/package_xz_5_0_5/9c92f8d0575b/package_xz_5_0_5 ) is causing the following error: File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.in

Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused

I took the rules directly from the Galaxy instructions page: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy and they worked in other servers. Anyway for some reason now it works. I disabled SELinux and it did and then it kept working even after I enabled it again. Turns out mod_rewrit