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gkno / gkno_launcher

The gkno launcher for executing tools or pipelines
MIT License
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Ubuntu 14.04.02 Installation Problems #57

Open prairie-guy opened 9 years ago

prairie-guy commented 9 years ago

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 commented 9 years ago

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 notifications@github.com 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.

— Reply to this email directly or view it on GitHub https://github.com/gkno/gkno_launcher/issues/57.