jimrperkins
commented
3 years ago Hi,
Thanks for your interest and well-described, informative message.
the source commands are just for us - we run the workflow in the supercomputer, so we have all the packages etc. described in the README already installed - we just need to use the source commands to load them.
In theory - if you have followed the README and installed everything, you would just need to comment the source commands and the workflow should run correctly - however, this may not actually be the case as there are many steps in the workflow and it is possible there is something we have overlooked in the README.
I'll get back to you later today or tomorrow with a dummy dataset.
Kindest regards
Jim
On Wed, 3 Feb 2021 at 05:15, lwz0324 notifications@github.com wrote:
Hi PhenCo authors I read with a great interest in your PLoS Genetics paper entitled "Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases" and would like to follow the line of thinking by doing some experiment on the topic. I have already read your instruction and installed the environment needed. However when I was running "launch_build_networks.sh", an error occured due to this command "source ~soft_bio_267/initializes/init_autoflow"，I don't know where to get the file "init_autoflow", "init_netanalyzer" and "init-pets". Could you give me some instructions? And I also don't know the correct format of input file. I tried to get the Data Access Agreement from DECIPHER but failed for some reason. Could you give me a sample of input file containing some patient data? It doesn't matter even if it is made up. I just want to validate whether this tool can work on my laptop so that I can use it to do some meaning analysis. Your assistance would be acknowleged in my research report and I look forward to hearing from you soon. Thank you very much!
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-- James R Perkins PhD Post-Doctoral Researcher, Rare Diseases Research Network (CIBERER) Department of Molecular Biology and Biochemistry https://goo.gl/maps/UCLQXZLR2W12 Science Faculty, University of Malaga 29071 Malaga, Spain
marklwzbupt
Hi PhenCo authors I read with a great interest in your PLoS Genetics paper entitled "Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases" and would like to follow the line of thinking by doing some experiment on the topic. I have already read your instruction and installed the environment needed. However when I was running "launch_build_networks.sh", an error occured due to this command "source ~soft_bio_267/initializes/init_autoflow"，I don't know where to get the file "init_autoflow", "init_netanalyzer" and "init-pets". Could you give me some instructions? And I also don't know the correct format of input file. I tried to get the Data Access Agreement from DECIPHER but failed for some reason. Could you give me a sample of input file containing some patient data? It doesn't matter even if it is made up. I just want to validate whether this tool can work on my laptop so that I can use it to do some meaning analysis. Your assistance would be acknowleged in my research report and I look forward to hearing from you soon. Thank you very much!