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Error Building GKNO due to tutorial retrieval failure #68
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Hi Chris, I'm unsure why downloading the tutorial data would have failed. Can you Please let me know if this doesn't work, or if you have any Al Alistair Ward, PhD Co-founder, Frameshift labs, LLC On Mon, Jun 20, 2016 at 2:00 PM, mcnaircm [email protected] wrote:
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Hey Alistair, |
That's strange. Do you have any odd firewalls or anything? I've tried doing Can you add other resources, e.g. ./gkno add-resource grch37? Alistair Ward, PhD Co-founder, Frameshift labs, LLC On Wed, Jun 22, 2016 at 12:07 PM, mcnaircm [email protected] wrote:
|
Hi Alistair, I have the same problem. I am repeated this installation a few times but I got to the same point. University of Utah gkno package version: 2.63.7 Checking dependencies...done. |
gkno has installed successfully. Only those tools marked as failed will not
be executable (i.e. pindel, mosaik, mutatrix and wham). These are not
common tools to use, so this should not present a problem to using the
majority of the gkno pipelines. If you type run the gkno executable file,
you should see that gkno runs and you can choose different pipelines to
run. Some help is provided at gkno.me, or you can contact me for specific
help and guidance.
Alistair Ward, PhD
Director, Research and Science
Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine
15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330
Co-founder, Frameshift labs, LLC
…On Fri, Nov 25, 2016 at 3:42 AM, hideoimamura ***@***.***> wrote:
Hi Alistair,
I have the same problem. I am repeated this installation a few times but I
got to the same point.
thank you,
Hideo
mac-C02N1289FH05:gkno_launcher himamura$ ./gkno build
========================================================
University of Utah gkno package
version: 2.63.7
date: November 2016
git commit: 0274e25
<0274e25>
Checking dependencies...done.
Initializing component data...
done.
Building tools:
bamaddrg...done.
bamtools...done.
bedtools...done.
blast...done.
bwa...done.
freebayes...done.
htslib...done.
samtools...done.
pindel...ERROR: See logs/build_pindel.* files for more details.
libStatGen...done.
bamUtil...done.
fastQValidator...done.
qplot...done.
verifyBamID...done.
mosaik...ERROR: See logs/build_mosaik.* files for more details.
mutatrix...ERROR: See logs/build_mutatrix.* files for more details.
picard...done.
samblaster...done.
seqan...done.
snpEff...done.
tabix...done.
tangram...done.
vcflib...done.
vt...done.
wham...ERROR: See logs/build_wham.* files for more details.
Fetching default resources:
tutorial:
Downloading files... 0%
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Hi Alistair, thank you for a quick response. |
Oh, I see. I'm confused with why some people observe this problem with
downloading the resources. Whenever I test it out, there is never any
problem with the resource downloading part. Do you see any logs that give
specific errors with this step? I wonder if you can try the following. Move
into the directory <path>/gkno_launcher/resources/tutorial, and type
wget http://marth-award.genetics.utah.edu:8089/version_10.tar.gz
Does this work? If not, what are the errors that you get? If you do get
this, let me know and we can fix up your version of gkno so that all the
pipelines can run the tests using the resources stored here.
Here is a quick fix so that you can start playing with gkno. Open the
following file:
<path>src/gkno/conf/user_settings.json
and you should see a line that says "isBuilt" : false. Just change the
'false' to 'true' and everything should run fine. You won't be able to use
any of the tools that failed to compile, or any of the "test" parameter
sets to test pipelines since you need the data in the tutorial resources
which you weren't able to download.
It is possible to add any tools you want into gkno, so if you have
executable versions of any tools not included, or of those tools that
failed, you can modify gkno to make them executable. I am working on a
couple of tutorials to help you add your own tools. Please let me know if
these would be useful, and I'll make an effort to finish them sooner rather
than later!
Al
Alistair Ward, PhD
Director, Research and Science
Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine
15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330
Co-founder, Frameshift labs, LLC
…On Fri, Nov 25, 2016 at 4:13 PM, hideoimamura ***@***.***> wrote:
Hi Alistair, thank you for a quick response.
When I type .
/gkno
ERROR: gkno not built.
Because
Downloading files... 0%
stops the building process every time I gkno build.
So gkno is not built successfully.
It always stops at
Downloading files... 0%
It does not go any further.
I worked at Boston college when Mike S was there and Gabor knows me as
well. I can run most of the programs by myself and I am just testing how
gkno works. So far I cannot test since it cannot be built.
Thank you.
Hideo
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I am currently having an issue in building gkno, and weirdly enough it seems to be with the retrieval of the tutorial after everything esle is done which terminates the process. The following is what I see when I try to run the build:
./gkno build [ 1:35PM]
University of Utah gkno package
version: 2.57.0
date: June 2016
git commit: de31cc5
Checking dependencies...done.
Initializing component data...done.
Building tools:
bamaddrg...done.
bamtools...done.
bedtools...done.
blast...done.
bwa...done.
freebayes...done.
htslib...done.
samtools...done.
pindel...done.
libStatGen...done.
bamUtil...done.
fastQValidator...done.
qplot...done.
verifyBamID...done.
mosaik...done.
mutatrix...done.
picard...done.
samblaster...done.
seqan...done.
snpEff...done.
tabix...done.
tangram...done.
vcflib...done.
vt...done.
wham...done.
Fetching default resources:
tutorial:
Downloading files... 0%ERROR: Could not retrieve file at http://marth-award.genetics.utah.edu:8089/version_10.tar.gz
ERROR: See logs/build_tutorial.* files for more details.
TERMINATED: Errors found in running gkno. See specific error messages above for resolution.
I'm not really sure why not having the tutorial file would terminate the whole process, but there you have it. Any help in figuring out how to get around this issue would be much appreciated!
Cheers,
Chris
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