gabaldonlab / karyon Goto Github PK
View Code? Open in Web Editor NEWThis is the Karyon Pipeline
License: GNU General Public License v3.0
This is the Karyon Pipeline
License: GNU General Public License v3.0
Hello,
I would like to use the pipeline for the mapping and variant calling, plotting but I would like to skip the first parts which are the assembly, reduction and proceed directly to the above steps. My assembly is already in a good state. However, bin/varcall_recipee.py does not come with documentation of the required arguments. Are the scripts also as a standalone version or does some one need to run the entire pipeline?
Thanks
Alex
Hi, I really like the nQuire plots included in this, and think those among the others could be really useful. I have the required files for the allplots.py script - vcf, pileup, etc - but cant get it working.
I am getting the following error message:
Traceback (most recent call last):
File "bin/allplots.py", line 100, in <module>
config_dict["KAT"][0],
KeyError: 'KAT'
I am running the following command:
python3 allplots.py \
-f redundans _reduced.fasta \
-v file.vcf -p file.mpileup \
-b file.bam \
-l library_to_make_fasta.fastq \
-o out_file
I have installed with both lightinstall.sh and install.sh and am getting the same message.
Can you help? I will try the docker image int he meantime, many thanks.
Hello, I am trying to install karyon. I am installing it on a cluster environment (without admin rights or apt or apt-get) mostly using conda. I am running into small things I am able to resolve, but I thought I should keep track of them as it might be useful for you.
1 - 6. are just some small observations I run into while going through the manual and trying to get the plot done.
7. is something I would like to bring your attention to, because I am reviewing the manuscript right now and the software should work beforehand.
I think this line in the installation script should be
conda install -c bioconda -y sra-tools
instead. Because as it is, I am getting
conda install: error: argument -c/--channel: expected one argument
I installed GATK4 via conda instead
conda install -c bioconda gatk4
I think sudo chmod 777 nQuire
can be simply chmod 777 nQuire
(sudo in unnecessary)
At this point, I gave up on most of the software, because all I wanted to generate are the karyon plots for the already assembled genome. It would be handy to have a reduced installation procedure for people that would like to do the genome on their own.
Some parts of the manual pdf are not well typeset - some of the spaces in the code are not there and when one copy-pastes a bit, it will mess up the command. And oddly enough, only some parts of the manual file have this problem.
all_plots.py
in the manual should be allplots.py
(at least that's the name of a script). Furtheremore, the script requires -p <pileup>
file, while manual instruct to specify -m example.mpileup
file (thought -p example.mpileup
actually did the job). It also screamed when I tried to specify it 2 sequencing files (R1 and R2).
then I finally managed to get it run, but then I got
python3 install/karyon/bin/allplots.py -f data/reference/genome.fa -v freebayes_Afus1_raw.vcf -p Afus1.mpileup -b data/mapped_reads/Afus1.rg.sorted.rmdup.bam -l data/trimmed_reads/Afus1/ERR5959256-trimmed-pair1.fastq.gz -o data/Afus1/karyon_plots
Traceback (most recent call last):
File "/scratch/kjaron/install/karyon/bin/allplots.py", line 93, in <module>
allplots(window_size,
File "/scratch/kjaron/install/karyon/bin/karyonplots.py", line 496, in allplots
os.mkdir(kitchen)
FileNotFoundError: [Errno 2] No such file or directory: '/home/karyon/tmp/6X0UH5'
I have not installed all the components, I have just thoseI thought will be necessary for the analysis (nQuire and all the python libraries). This is something I would like to propose as well - could you perhaps create simpler installation instructions for people interested in the ploidy analysis and plots from existing assembly/vcf files?
Hi, i think that the nQuire ploidy/CN plots look great. Would you be able to pull them out as a standalone script i could use please?
Ive spent a lot of time trying to get the allplots.py script running but have had no luck yet.
Many thanks
Mike
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.