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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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how to load roary data into panx #525

Open taffners opened 3 years ago

taffners commented 3 years ago

Hello,

On the roary website it mentions that panx can be used to visualize the data. I'm trying to load data into panx like the panx website says but the roary output is not recognized. I'm following the instructions here [https://github.com/neherlab/pan-genome-visualization/#add-your-own-data](add your own data).

It keeps on erroring out on link-to-server.py. Here are two of the methods I tried. I have the output of roary in the roary_default folder where I ran roary on default settings.

python link-to-server.py -s /gpfs/fs2/scratch/staffner/pan-genome-visualization/cdiff_6month_roary/roary_default -v /scratch/staffner/pan-genome-visualization rsync: change_dir "/gpfs/fs2/scratch/staffner/pan-genome-visualization//./data//gpfs/fs2/scratch/staffner/pan-genome-visualization/cdiff_6month_roary/roary_default/vis" failed: No such file or directory (2) rsync: mkdir "/scratch/staffner/pan-genome-visualization/public/dataset//gpfs/fs2/scratch/staffner/pan-genome-visualization/cdiff_6month_roary/roary_default" failed: No such file or directory (2) rsync error: error in file IO (code 11) at main.c(657) [Receiver=3.1.2]

python link-to-server.py -s /gpfs/fs2/scratch/staffner/pan-genome-visualization/cdiff_6month_roary/roary_default/gene_presence_absence.csv -v /scratch/staffner/pan-genome-visualization rsync: change_dir "/gpfs/fs2/scratch/staffner/pan-genome-visualization//./data//gpfs/fs2/scratch/staffner/pan-genome-visualization/cdiff_6month_roary/roary_default/gene_presence_absence.csv/vis" failed: No such file or directory (2) rsync: mkdir "/scratch/staffner/pan-genome-visualization/public/dataset//gpfs/fs2/scratch/staffner/pan-genome-visualization/cdiff_6month_roary/roary_default/gene_presence_absence.csv" failed: No such file or directory (2) rsync error: error in file IO (code 11) at main.c(657) [Receiver=3.1.2]

Thank you for your help. Samantha

leabact commented 2 years ago

Hello, i have the same issue here. Would be helpful to know what's supposed to be in the "vis" file that link-to-server is searching for, so maybe we can copy of roary results to it's taken into account