Hi Roberto,
It looks like this is a known issue with FASTQ splitting,
https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-parallelism
I originally broke it during a refactor, but it looks like the
discussion died about that that method was meant to do
(e.g. FQTOC = FASTQ table of contents?
Hi,
Thanks for the tips, Peter. Hmm. No amount of playing with my
galaxy-dist/tool_conf.xml.sample file is enabling the tool to be found by
run_tests.sh . In the run_functional_tests.html I see:
File "/usr/lib64/python2.6/unittest.py", line 278, in run
testMethod()
File
"/usr/local/
It may be possible to do this using a select field plus dynamic
options. The cummeRbund tool seems to use a select that uses arbitrary
Python to generate options - but I may be missing something.
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummeRbund
If it really does that -
Hi Nikos,
can you provide us your tool_dependencies.xml file please?
Thanks,
Bjoern
Am 11.02.2015 um 17:27 schrieb Nikos Sidiropoulos:
> Hi all,
>
> I have a package repository that installs an R package and another
> repository with a set of tools that use that package repository.
>
> Tools t
Glad it passed!
And, yes, it should. I'd planned on getting it over there today.
On Thu, Feb 12, 2015 at 10:59 AM, Nicola Soranzo
wrote:
> Yes, the TravisCI build passed again.
> Thanks a lot Dannon!
>
> Should this commit go also to stable branch?
> Nicola
>
> Dannon Baker ha scritto ---
Yes, the TravisCI build passed again.
Thanks a lot Dannon!
Should this commit go also to stable branch?
Nicola
Dannon Baker ha scritto
> I believe I've fixed this in 16583:5b2f1eab2819, if you want to give it
> another shot. External version of pkg_resources (and not ours in lib/) is
Hello,
You probably need to reassign the datatype to be "fastqsanger", but double
check the quality score scaling first. You FastQC run will be part of this.
Our wiki has the details here, sections 2.9 & 2.10.1
http://wiki.galaxyproject.org/Support
Best,
Jen
Galaxy team
On Wed, Feb 11, 2015 at 1
Maybe its the same issue as posted here?
https://biostar.usegalaxy.org/p/3877/#3879
"The datatype for your dataset must be set to fastqsanger"
Stef
- Original message - From: "Xiong, Min," To:
"galaxy-dev@lists.galaxyproject.org"
Subject: [galaxy-dev] BWA alignment
problem in Galaxy D
Hi all,
I have a package repository that installs an R package and another
repository with a set of tools that use that package repository.
Tools that use an Rscript command interpreter load that module
successfully, e.g.:
"normalize.xml"
R_3_1_1
RNAprobR
RNAprobR
I believe I've fixed this in 16583:5b2f1eab2819, if you want to give it
another shot. External version of pkg_resources (and not ours in lib/) is
what was causing the weird egg fetching errors. Newer versions of
pkg_resources create a mangled distribution string for some eggs with
nonstandard ver
Hi Stephen and Nate,
it seems that the problem with the WebError egg
is now hitting also BioBlend TravisCI
testing:
https://travis-ci.org/galaxyproject/bioblend/builds/50391748
Both
for Python 2.6 and 2.7, scripts/common_startup.sh fails
with:
"WebError 0.8a couldn't be downloaded automaticall
On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion wrote:
> I was trying to track down why an attempt to test my tool is eventually
> failing with:
>
> "ValueError: No such test TestForTool_ffp_phylogeny"
>
There are at least two reasons that can happen.
(a) The tool wasn't loaded by the test fram
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