Error Building GKNO due to tutorial retrieval failure

[mcnaircm]

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: de31cc53dad6c57e73a2d7e8110487f10339abdb

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

[AlistairNWard]

Hi Chris,

I'm unsure why downloading the tutorial data would have failed. Can you access the data by just trying a wget (e.g. wget http://marth-award.genetics.utah.edu:8089/version_10.tar.gz)? If you can, maybe there was an odd error when you tried the build and you can just try and rebuild gkno. Either way, you're right that failure to get the resources shouldn't stop you being able to run gkno since everything else is actually available (although none of the 'test' parameter sets in the pipelines would work). I have updated the code, to ensure that the final configuration file is still created on failure to download resources ensuring that gkno will still run. Please try recloning and build again and even if the resource download fails, gkno should still be executable.

Please let me know if this doesn't work, or if you have any questions/comments about using gkno.

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 Mon, Jun 20, 2016 at 2:00 PM, mcnaircm notifications@github.com wrote:

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 https://github.com/gkno/gkno_launcher/commit/de31cc53dad6c57e73a2d7e8110487f10339abdb

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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[mcnaircm]

Hey Alistair, I probably should have said in the initial post but I did in fact attempt to do this when I had the issue initially and I keep getting a connection time out error when I try to wget the tutorial directly. I re-cloned gkno and although the tutorial still didn't download it seems that gkno will run now! Thanks!

[AlistairNWard]

That's strange. Do you have any odd firewalls or anything? I've tried doing a build and getting the resources myself a couple of times to check and have no problems getting the resources to download.

Can you add other resources, e.g. ./gkno add-resource grch37?

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 Wed, Jun 22, 2016 at 12:07 PM, mcnaircm notifications@github.com wrote:

Hey Alistair, I probably should have said in the initial post but I did in fact attempt to do this when I had the issue initially and I keep getting a connection time out error when I try to wget the tutorial directly. I re-cloned gkno and although the tutorial still didn't download it seems that gkno will run now! Thanks!

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[hideoimamura]

Hi Alistair, I have the same problem. I am repeated this installation a few times but I got to the same point. And because the installation stops there, I cannot install the entire packet. Can I skip this downloading?
thank you, Hideo mac-C02N1289FH05:gkno_launcher himamura$ ./gkno build

University of Utah gkno package

version: 2.63.7 date: November 2016 git commit: 0274e25cdbfe8e892a1db1f29b31d4f99d451758

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%

[AlistairNWard]

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 notifications@github.com 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 https://github.com/gkno/gkno_launcher/commit/0274e25cdbfe8e892a1db1f29b31d4f99d451758

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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[hideoimamura]

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

[AlistairNWard]

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 /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:

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 > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . >