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
Happy New Year from the Galaxy Project!
January https://wiki.galaxyproject.org/GalaxyUpdates/2015_01 brings lots
of Galaxy related news
https://wiki.galaxyproject.org/GalaxyUpdates/2015_01, including
-
63 new papers
https://wiki.galaxyproject.org/GalaxyUpdates/2015_01#New_Papers,
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:
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
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
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 jmchil...@gmail.com wrote:
It is certainly the case that Galaxy should be using the latest
version of
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
On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock p.j.a.c...@googlemail.com 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
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 http://gcc2015.tsl.ac.uk/training-day/ page for what's been nominated
so far, and for a link to the nomination form.
If you want
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
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
I could be wrong but I think the install 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
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