Re: [galaxy-dev] GCC2015 Training Day Topic Nominations are Open through January 6

Hello all, Just a reminder that GCC2015 Training Day Topic Nominations *close Tuesday, 6 January, which might be today by the time you see this. *See the Training Day page for what's been nominated so far, and for a link to the nomination form. If you wan

Re: [galaxy-dev] Problem with Biopython

On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock wrote: > Yes ;) > > Are you writing your own tool, or trying to install someone else's? > > There are two basic options, > > (1) Install Biopython into the default Python used when jobs are > run. Simple, but manual - and you can only have one version. >

Re: [galaxy-dev] Problem with Biopython

Yes ;) Are you writing your own tool, or trying to install someone else's? There are two basic options, (1) Install Biopython into the default Python used when jobs are run. Simple, but manual - and you can only have one version. This is actually what we are still doing on our local Galaxy since

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Ryan, I have tried to collect a minimal set of dependencies you need to have installed: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList And we have a Galaxy Docker container that is working and should define and test a fresh Galaxy installation: https://github.com/bgruening/

Re: [galaxy-dev] Mercurial is out of date for Toolshed

Hi Ryan, unfortunately not (yet). But I'm really surprised you are getting this error. It working for me and in our docker containers and other deployments. Can we try to detect the root cause of this error? Do you have conflicting mercurial version. Cheers, Bjoern > Thanks. Is there an alterna

Re: [galaxy-dev] Problem using FastQC in Galaxy

I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves. One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single platform

[galaxy-dev] Text file busy

I get this error occasionally: "/bin/sh: 1: /opt/galaxy/web/database/job_working_directory/000/100/galaxy_100.sh: Text file busy" When this occurs, the step fails outright. Resubmitting the step resolves the issue and things run no problem. If this error appears early in a long workflow, I have

Re: [galaxy-dev] Mercurial is out of date for Toolshed

Thanks. Is there an alternative way I can install tools from the Toolshed? This problem pretty much renders the toolshed unusable for me... On Mon, Jan 5, 2015 at 11:14 AM, John Chilton wrote: > It is certainly the case that Galaxy should be using the latest > version of mercurial given a numb

[galaxy-dev] Web/Job scaling question

Hello, Current setup: : have 1-2 VMs w/ 4-core each, 4GB mem mounting remote lustre shared fs : use remote job submission: cli/ssh : proxied, use remote auth login/logout I'm prepping for a scenario where there will be 60-75 users/students who will simultaneously submit several complete

Re: [galaxy-dev] Create a package with binaries

I could be wrong but I think the tag should have some sort of download action - I don't think tools are actually stuck in $INSTALL_DIR like this - $INSTALL_DIR is where you can move or compile downloaded files to. You might want to try $REPOSITORY_INSTALL_DIR instead of $INSTALL_DIR - but really i

Re: [galaxy-dev] Problem using FastQC in Galaxy

We reverted back to fastqc version 0.10.1 and that is working. Given that our current galaxy version is old and problematic to upgrade, going forward we're going to stand up a new separate galaxy installation on another server. We'll be able to test everything on it before switching over to it.

Re: [galaxy-dev] Problem using FastQC in Galaxy

Thanks :) 2015-01-05 16:45 GMT-02:00 Björn Grüning : > Hi, > > why do you need biopython for FASTQC? > You can install biopython from the ToolShed and can depend on it: > > https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64 > > Cheers, > Bjoern > > Am 05.01.2015 um 19:01 schrieb

Re: [galaxy-dev] Creating a new job handler for Galaxy

This sounds like a fun and challenging project - good luck! The route I would recommend pursuing largely hinges on whether all 5 Galaxy instances have a shared file system and run as a single user. If they do I would recommend implementing a Galaxy "job runner" - all the runners bundled with Galax

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi, why do you need biopython for FASTQC? You can install biopython from the ToolShed and can depend on it: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64 Cheers, Bjoern Am 05.01.2015 um 19:01 schrieb Alfredo Guilherme Silva Souza: > Has anyone used the Biopython in Galaxy

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hey Alfredo, You shouldn't have to mess with eggs for tools -- those are primarily dependencies of the core framework itself. Do you have biopython installed and available in the environment (PYTHONPATH) of whatever user jobs are run as? That is, if you open a plain python shell as the galaxy us

[galaxy-dev] Problem with Biopython

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in * *import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in

Re: [galaxy-dev] galaxy.tools.parameters.basic.RuntimeValue not str

It looks like the workflow submission code was unable to map your parameter "reference_genome|index" to the correct tool runtime value. Is there any chance you can post the tool and/or the workflow? Also - I am assuming here the tool_id is mapper_easy - is that correct? -John On Fri, Jan 2, 2015

[galaxy-dev] Problem using FastQC in Galaxy

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in * *import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in

[galaxy-dev] January 2015 Galaxy News!

Happy New Year from the Galaxy Project! January brings lots of Galaxy related news , including - 63 new papers ,

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Michael, I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks pr

Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?

That post looks like it might be wrong. If 21 is the step id of the tool (edgeR) then ds_map should probably reference steps 19 and 20 right? Also - I will see what I can do about improving these workflow API error messages - it is never exactly clear to me what is wrong when there are problems.

Re: [galaxy-dev] Mercurial is out of date for Toolshed

It is certainly the case that Galaxy should be using the latest version of mercurial given a number of high profile bugs with older versions. Unfortunately it doesn't seem possible to just drop the new version it - there are some API changes that prevent Galaxy from loading when doing this and the

Re: [galaxy-dev] Problem using FastQC in Galaxy

Ok, we have run several previous version of fastqc with it, we'll try one of those. Our history of galaxy upgrade attempts has been very problematic. Things always seem to break, items disappear from menus, and I'm lost in trying to figure out the problems, so we tend to leave it alone. Mike

Re: [galaxy-dev] run_test.sh - ImportError: cannot import name _args_from_interpreter_flags

Hey Ryan, This happens to me every time (or nearly every time) I run tests as well and with no bearing on whether the test succeeds or not - so I suspect this is not a serious problem. I am not sure what the problem is but it seems to be a bug in Python itself. Are you testing specific tools or G

Re: [galaxy-dev] Problem using FastQC in Galaxy

This looks like a bug - but unfortunately it appears you are running a fairly old version of Galaxy - I don't think the file lib/galaxy/util/shed_util.py has existed for the better part of a year. It should be possible to get the FastQC wrapper to work with the old version if you figure out the ex

Re: [galaxy-dev] Visualization in anonymous mode ?

Hi, Loraine At this time there is no way to activate visualizations for anonymous users. The logged-in user data is required by most visualizations for some features to work (e.g. saving visualizations, publishing, etc.). In the future, it might be possible to de-couple these systems and provide

Re: [galaxy-dev] Problem using FastQC in Galaxy

I attempted to install fastqc via the tool shed, and got an error. The log information is listed below. The main error appears to be "too many values to unpack". 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&r

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Mike, give it a shot for sure. If you want some details have a look at https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial M. On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H wrote: > It's mostly due to my lack of thorough knowledge about Galaxy. So should I > just try

[galaxy-dev] Creating a new job handler for Galaxy

Hi Galaxy developers, In our Elixir project (http://www.elixir-europe.org/), Norway, we have five geographically distributed Galaxy instances. Each is working on a local cluster (mostly SLURM). We are planning to interconnect those five clusters using a meta-scheduler ARC (http://www.nordugrid