Ubuntu 14.04.02 Installation Problems

[prairie-guy]

gkno_lanuncher fails to build all the tools on a vanilla Ubuntu 14.04.02 (64-bit) running in vmware. Most notable was jellyfish. I was ultimately able to install all the tools with the following commands:

sudo /usr/bin apt-get install git ant cmake gcc g++ make openjdk-7-jdk ruby
sudo /usr/bin/ apt-get build-dep samtools valgrind bwa samtools
git clone https://github.com/gkno/gkno_launcher.git
cd gkno_launcher
./gkno build

Even so, './gkno run-test' fails.

[AlistairNWard]

Thanks for this feedback. While a large number of dependencies are checked,
I haven't managed to get everything required by all tools to be checked
yet. We are also working on getting a Docker container available that has
everything compiled, but this is not yet available. Thanks for persisting
and getting everything compiled manually and I'll make sure to keep a note
of the other dependencies you had to install and get an upfront check
included.

As for the ./gkno run-test pipeline - this was removed some time ago. I am
in the process of updating the web resources and will have more
comprehensive help and tutorials available in the near future. If there are
specific issues, please let me know and I'll get to those first! You can
see all of the currently available pipelines using ./gkno -api, or look at
categories using ./gkno -cat. All pipelines can be build with 'parameter
sets'. These are sets of commonly used parameter sets that can all be set
by just defining the parameter set. If you look at the help for any
individual pipeline, you should see a list of the available parameter sets.
To test any pipeline, use the 'test' parameter set, e.g.:

./gkno freebayes -ps test

This should run using files in the gkno_launcher/resources/tutorial/current
directory, and produce a compressed and indexed vcf file.

Please do not hesitate to contact me with questions/concerns or suggestions.

Al

On Mon, Jul 27, 2015 at 10:21 AM, prairie-guy [email protected]
wrote:

gkno_lanuncher fails to build all the tools on a vanilla Ubuntu 14.04.02
(64-bit) running in vmware. Most notable was jellyfish. I was ultimately
able to install all the tools with the following commands:

sudo /usr/bin apt-get install git ant cmake gcc g++ make openjdk-7-jdk ruby
sudo /usr/bin/ apt-get build-dep samtools valgrind bwa samtools
git clone https://github.com/gkno/gkno_launcher.git
cd gkno_launcher
./gkno build

Even so, './gkno run-test' fails.

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