[galaxy-dev] Help with dynamic job destination

2016-03-15 Thread Lance Parsons
I'm trying to setup a dynamic job destination for bowtie2 so that it submits to a different destination if the `-a` option is set or the `-k` option is set to a high value. I've got things working, but the function I've written seems rather complicated and ugly. I was wondering if anyone had

Re: [galaxy-dev] Please help fix toolshed repository: trtr

2016-03-15 Thread Martin Čech
Hi Lance, it seems the whole .git/ folder got accidentally uploaded there and it causes trouble. I recommend using the direct mercurial access ( https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the folder, commit the change and push it to the TS repository. Please let me know how it

Re: [galaxy-dev] Job stuck in running state.

2016-03-15 Thread John Chilton
What kind of database backend are you using (postgres, myql, or the default sqlite)? If you are running many jobs - I would definitely encourage using postgres. -John On Sun, Mar 13, 2016 at 2:48 PM, Zuzanna K. Filutowska wrote: > Dear All, > > I am running newest

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

2016-03-15 Thread Bjoern Gruening
Saw it! Will review it today, this looks really nice! On 15.03.2016 08:28, Léo Biscassi wrote: Hi Bjorn, I've created the pull request [1] in your repository. I will be grateful if you can assist me with the functional tests on the docking tool and the final validation of the tool

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

2016-03-15 Thread Léo Biscassi
Hi Bjorn, I've created the pull request [1] in your repository. I will be grateful if you can assist me with the functional tests on the docking tool and the final validation of the tool dependencies. [1] https://github.com/bgruening/galaxytools/pull/310 Thanks a lot! Best regards, On Mon, Mar

Re: [galaxy-dev] Problems uploading files to galaxy

2016-03-15 Thread John Chilton
If you are running jobs as "the real user" with drmaa (using the chown script) - you will probably want to setup a separate job destination using the local runner for upload jobs. The upload tool uses files that are created outside of Galaxy and these aren't modeled well. Does this help? -John

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

2016-03-15 Thread Rathert , Philipp , Dr .
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

Re: [galaxy-dev] external_chown_script.py and the local job runner

2016-03-15 Thread Peter Cock
On Mon, Jan 25, 2016 at 4:59 PM, Peter Cock wrote: > On Mon, Jan 25, 2016 at 4:44 PM, John Chilton wrote: >> I think the problem is more that it is configured globally and not >> per-destination. The real user stuff should all be per-destination

Re: [galaxy-dev] Problems uploading files to galaxy

2016-03-15 Thread Peter Cock
On Tue, Mar 15, 2016 at 2:21 PM, John Chilton wrote: > If you are running jobs as "the real user" with drmaa (using the chown > script) - you will probably want to setup a separate job destination > using the local runner for upload jobs. The upload tool uses files > that

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

2016-03-15 Thread Léo Biscassi
Hi, thanks for the considerations in the code, I'll make the changes later. The packages Autodock Vina and MGL Tools works fine!? I saw that tests passed with success on Travis. Cheers, On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening wrote: > Saw it! Will review it

Re: [galaxy-dev] Problems uploading files to galaxy

2016-03-15 Thread Lemley, Rob
Thanks Peter, that's really helpful. I'm glad we're not the only ones running into this. -Rob Rob Lemley Systems Administrator – CIRC University of Rochester -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Tuesday, March 15, 2016 10:34 AM To: John Chilton

[galaxy-dev] Trackster in 16.01 broken

2016-03-15 Thread Lubos Klucar
Hi, after upgrading from 15.10 to 16.01, the trackster visualisation tool is partly defective. It can successfully show e.g. GFF tracks, but after adding e.g. BAM track nothing is shown. The only suspicious debug output I could get when loading non-working-track is:

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

2016-03-15 Thread Bjoern Gruening
On 15.03.2016 18:11, Léo Biscassi wrote: Hi, thanks for the considerations in the code, I'll make the changes later. The packages Autodock Vina and MGL Tools works fine!? I saw that tests passed with success on Travis. No, not really. You need to create a .shed.yml file to trigger the

Re: [galaxy-dev] Trackster in 16.01 broken

2016-03-15 Thread Marius van den Beek
Hello Lubos, this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897. If you pull in the latest changes (`git pull`) on the release_16.01 branch things should work again. Cheers, Marius On 15 March 2016 at 18:59, Marius van den Beek wrote: > Hello

Re: [galaxy-dev] Trackster in 16.01 broken

2016-03-15 Thread Lubos Klucar
Dear Marius, thanks for help, but it looks our galaxy is up to date: remote: Counting objects: 111, done. remote: Compressing objects: 100% (23/23), done. remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13 Receiving objects: 100% (111/111), 39.85 KiB, done. Resolving deltas:

Re: [galaxy-dev] Problems uploading files to galaxy

2016-03-15 Thread Lemley, Rob
Hi John, Thanks for getting back to me. If I'm understanding the XML files correctly, the upload tool is already configured to run as a local job. From job_conf.xml: where "local" is our local job runner and "upload1" is defined in data_source/upload.xml. -Rob Rob Lemley Systems

Re: [galaxy-dev] Trackster in 16.01 broken

2016-03-15 Thread Marius van den Beek
Hello Lubos, this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897. If you pull in the latest changes (git pull) on the release_16.01 branch things should work again. Cheers, Marius On 15 March 2016 at 18:54, Lubos Klucar wrote: > Hi, > > after

Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

2016-03-15 Thread Chris Dagdigian
Hi Ryan, I've never been able to get cloudman to function within a private VPC so if this is your architecture as well and you manage to make progress I'd be interested in learning your methods. Thanks! Regards, Chris Enis Afgan wrote: Hi Ryan, I'm not sure I really understand your

Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

2016-03-15 Thread Enis Afgan
Hi Ryan, I'm not sure I really understand your question but CloudMan can run under an IAM account - it is just necessary to give the IAM user permissions to create EC2 and S3 resources. Let us know if that's not what you had in mind or if you have any more questions. Cheers, Enis On Mon, Mar 14,

Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

2016-03-15 Thread Ryan G
We actually have galaxy running within a VPC now. The problem we're running into is that when ec2 instances get created they don't have an I_am profile attached to them so they can't get access to S3 resources. This should just be a parameter past to AWS when the instances get created to attach

Re: [galaxy-dev] Trackster in 16.01 broken

2016-03-15 Thread Marius van den Beek
Hi Lubos, I opened a Pull Request on https://github.com/galaxyproject/galaxy/pull/1930, which should hopefully fix the problem. If you want to give it a try, you can do `git fetch origin pull/1930/head:more_bytestring_for_pysam` and `git checkout more_bytestring_for_pysam`. When the problem has