Hi,
One of my users is trying to use the clustered heatmap feature and we
are getting the following error:
/data/homes/galaxy/galaxy/dependencies/R/3.0.3/iuc/package_r_3_0_3/a8438aa1207c/lib/R/bin/exec/R:
error while loading shared libraries: libgfortran.so.1: cannot open
shared object file: No s
Hi Scott,
you can try to reinstall it with: "Admin" -> "Manage installed tools",
then click on "Advanced Search" on top, then click on "Deactivated or
uninstalled" and click on "Activate or reinstall" on Trimmomatic menu.
Cheers,
Nicola
On 20/11/15 18:07, Scott Szakonyi wrote:
Hi Nicola,
Ce
Hi Nicola,
Certainly. On screen, I get a message that says "Revision *f8a9a5eaca8a* of
repository *trimmomatic* owned by *pjbriggs* has already been installed."
In the logs:
129.74.33.163 - - [20/Nov/2015:12:51:44 -0400] "GET
/admin_toolshed/browse_repositories?status=error&message=Revision+%3Cb
Hi all,
If I try to build a new track browser from a custom build, I'm not able to
see any of the datasets in my build after clicking add datasets and
selecting my workflow from history. Am I doing something wrong, or is there
a problem? I've been able to recreate this on both my local server and
Hi Scott,
can you try to update Trimmomatic (i.e. go to "Admin" -> "Manage
installed tools" and click on "Install latest revision" on Trimmomatic
menu) ?
If this does not work, copy the relevant log from the Galaxy server and
post it on the mailing list.
Cheers,
Nicola
On 20/11/15 17:23, Sco
I was able to switch over to GitHub without issue. Thanks for pointing me
in the right direction.
I have installed Trimmomatic successfully, although I wasn't able to
install the latest version. If I try to install the "2015-09-23" revision,
I get "Internal Server Error Galaxy was unable to succes
DVCSs are weird - 1aecca7889681ad9518e26e2a62b470809d2cdd1 is a single
commit that is in dev from a week ago but its parent is from dev on
October 11 (that is when the branch was forked). So it actually
doesn't have the recent huge switch from eggs to wheels that broken
everything.
For instance, t
Hi Scott,
please always reply to the mailing list, because I may not be able to
solve your issues.
I was able to install the latest revision of Trimmomatic without issues,
so we may need some more information from the Galaxy logs to understand
what is your issue.
Same for the other repositor
Confirmed with a fresh galaxy checkout
commit 05ed245353331489ee443ac483b1569dab38f500
Author: Dannon Baker
Date: Thu Nov 19 20:48:16 2015 -0500
Then ran sh.run.sh to get the updates
without the additions to requirements.txt Planemo fails.
Added the four lines.
restarted the server with sh r
Hi John,
Yes i have vitrualenv installed.
I tried planemo both using :
brew tap galaxyproject/tap
brew install planemo
And using:
virtualenv .venv; . .venv/bin/activate
pip install planemo
With the exact same results
I also have not trouble running galaxy without the extra. bit in galaxy's
re
Do you have virtualenv installed and available to planemo? If not,
might be worth reviewing this thread -
http://dev.list.galaxyproject.org/Planemo-0-20-0-and-xunit-td4668334.html
and installing it.
In dev, virtualenv is a hard dependency for running Galaxy and this is
new, in the past Galaxy woul
I'll update planemo to explicitly check for virtualenv before running
Galaxy and give a very clear error message in this scenario.
I guess I could even make it an explicit dependency of planemo in
setup.py/PyPI - I wonder if it would be okay for planemo to mask the
OS virtualenv when installing vi
Hi Scott,
the mercurial mirror is not up to date unfortunately, see this previous
discussion:
http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html
Cheers,
Nicola
On 20/11/15 13:13, Scott Szakonyi wrote:
Hi Nicola,
I'm not entirely sure which version... bu
Just as a follow up on this for everyone using the workflow API, I
have opened a WIP PR to completely replace step ids with the step
order index in the workflows API so this confusion won't occur anymore
and the deprecated and modern endpoints work much more similarly:
https://github.com/galaxypro
I have gotten past this stage and an now getting errors which may be my own.
The fix was to edit
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/requirements.txt
and add
twill==1.8.0
lxml==3.5.0
cssselect==0.9.1
NoseHTML==0.4.2
There may well be other missing as well so t
I was referring to Galaxy's requirements .txt
This appears to be an issue with changes made to galaxy last weekend.
The very same Planemo work with
commit 1aecca7889681ad9518e26e2a62b470809d2cdd1
Author: Björn Grüning
Date: Sat Nov 14 23:56:19 2015 +0100
But fails at or BEFORE
commit b19e7
Which file are you looking at? There is no nose entry here:
https://github.com/galaxyproject/planemo/blob/master/requirements.txt
Perhaps a more recent version of nose is needed?
Peter
On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer
wrote:
> Hi Peter/ John
> requirementx.txt already
Hi Peter/ John
requirementx.txt already includes the latest version of nose
nose==1.3.7
It is nose that is complaining it does not like the sys,args passed in by
FunctionalTest.py
Christian
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Friday, Nov
On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer
wrote:
> Hi All,
>
> I am unable to run Planemo against the latest dev branch.
>
> 1. import twill error
>
> I was able to fix this by adding to requirements.txt
> twill==1.8.0
> lxml==3.5.0
> cssselect==0.9.1
>
> But then I get
>
> functio
Hi All,
I am unable to run Planemo against the latest dev branch.
1. import twill error
I was able to fix this by adding to requirements.txt
twill==1.8.0
lxml==3.5.0
cssselect==0.9.1
But then I get
functional_tests.py: error: no such option: --with-nosehtml
functional_tests.py ERROR 2015-11-20
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