Re: [galaxy-dev] conversion issue

Since I am using Galaxy-docker I am not sure how to get this installed... Always grateful for help. Cheers, Philipp -Original message- From: Rathert, Philipp, Dr.  Sent: Friday 5th August 2016 16:26 To: Peter Cock Cc: Brad Chapman ; galaxy-dev@lists.galaxyproject.org Sub

Re: [galaxy-dev] conversion issue

01.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" ==> /home/galaxy/logs/slurmctld.log <== [2016-08-05T14:25:30.946] completing job 7 [2016-08-05T14:25:30.947] sched: job_complete for JobId=7 successful, exit code=0 ==> /home/galaxy/logs/slurmd.log <== [2016-08-05

Re: [galaxy-dev] conversion issue

m via the Tool Shed? Peter On Fri, Aug 5, 2016 at 2:23 PM, Rathert, Philipp, Dr. mailto:philipp.rath...@ibc.uni-stuttgart.de> > wrote: > Dear All, > > > I get the following errors when I try to Convert BAM to BigWig > > > Traceback (most recent call last): >

[galaxy-dev] conversion issue

Dear All, I get the following errors when I try to Convert BAM to BigWig Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 103, in main(*args, **kwargs) Fil

[galaxy-dev] package_cython_0_20_1

Dear all, I am trying to install package_cython_0_20_1 but I always get the following error. It looks like the link is broken. Any ideas how to get this installed? Thanks for the help. Cheers, Philipp NameVersion TypeStatus Error cython

[galaxy-dev] Docker for Mac

Dear all I was wondering if anybody has experience running a galaxy production server using docker for mac. I know it's beta testing at the moment but since the Virtual machine environment gave us such a hard time preserving and managing user data etc. I thought I try it anyway... However, i

Re: [galaxy-dev] Infinite recursion on conda dependency manager

: Monday 20th June 2016 13:21 To: Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org Cc: Björn Grüning Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager Hi Philipp, you are inside of the Docker container? Can you do a: export PATH=/galaxy-central/tool_deps/_conda

Re: [galaxy-dev] History is not up-to-date

Dear Nicola, I am using the 16.04 release. did you implement changes in this one recently? Cheers, Philipp -Original message- From: Nicola Soranzo  Sent: Monday 20th June 2016 12:16 To: Rathert, Philipp, Dr. ; 'Carl Eberhard' Cc: galaxy-dev@lists.galaxyproject.org S

Re: [galaxy-dev] History is not up-to-date

mail.com] Sent: Tuesday, June 14, 2016 6:24 PM To: Rathert, Philipp, Dr. Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date   Hi, Phillip   Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser?

[galaxy-dev] History is not up-to-date

Dear All, I have a problem with my histories.  We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 -

Re: [galaxy-dev] cleanup datasets error

opg2 ImportError: No module named psycopg2 Can I install the python-psycopq2 module via apt-get in the container and would this help to fix thee issue? Cheers, Philipp -Original message- From: Rathert, Philipp, Dr.  Sent: Tuesday 14th June 2016 9:56 To: Bjoern Gruening Cc: galaxy-

Re: [galaxy-dev] cleanup datasets error

postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path = > /export/galaxy-central/database/files| > > Or is this broken? Cheers, Bjoern > > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote: > > Dear all, > > > > when I want to start the cleanu

[galaxy-dev] cleanup datasets error

Dear all, when I want to start the cleanup datasets script I get the following error. (.venv)root@galaxy:/galaxy-central# python /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -10 -1 Traceback (most recent call last):   File "/galaxy-central/scripts/cl

Re: [galaxy-dev] perl version 5.18.1 repository error

ent: Wednesday 23rd March 2016 12:49 To: Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] perl version 5.18.1 repository error Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage instal

[galaxy-dev] perl version 5.18.1 repository error

Dear all, i am trying to install  tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that  package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_per

Re: [galaxy-dev] shed_tool_conf.xml

- From: Peter Cock  Sent: Tuesday 22nd March 2016 12:56 To: Rathert, Philipp, Dr. Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] shed_tool_conf.xml I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the

[galaxy-dev] shed_tool_conf.xml

Dear all, I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools. Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file...

[galaxy-dev] Tool-install error with yaml file

Dear all, I want to install a bunch of tools using the install-tools function. In my yaml file tool.yml i have specified the url if my docker instance wit the ip adress i use in the web browser and the api_key is admin When i run install-tools tool.yml I get the error below and nothing happens.

Re: [galaxy-dev] cleanup

Dear Nicola, thanks it worked.  cheers, Philipp -Original message- From: Nicola Soranzo  Sent: Tuesday 23rd February 2016 20:35 To: Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] cleanup Hi Philipp, please alway reply to the mailing

[galaxy-dev] Docker and issue with shed_tool_conf.xml

Dear All,  I have a serious problem with installing new tools to our local Docker-galaxy-stable instance (latest version). All tools seem to install without any issue from the tool shed. When I check under Manage installed tools they all show a green "installed" button. However, the local

Re: [galaxy-dev] NGS.plot script freeze

Hi Björn, The browserpage freezes. And after some time it says: script freeze, debug or stop? I do not manage to start the tool or even see the tool page. Cheers, Philipp Am 13.02.2016 um 17:18 schrieb Björn Grüning mailto:bjoern.gruen...@gmail.com> >: Hi Phillipp, what means the script fre

[galaxy-dev] CEAS error

Dear All, We are running a local docker-galaxy-stable instance on a Mac OS X system. and observe a strange error: CEAS  Description:  Revision:f411ce97a351 is not installing correctly. After installing mysql-python in the container directly basically every package is installed: Installe