ryao-mdanderson
commented
2 years ago Hello Roary support team:
I find this docker command makes a little move on, however, I would like to hear your suggestion to provide a meaningful test.
$ docker run --rm -it -v $HOME/roary_test/3.13/t/data/accessory_graphs:/data docker.io/sangerpathogens/roary roary -f . /data/file_1.gff /data/file_2.gff
Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Pubmed: 26198102
2022/01/19 04:43:24 Could not extract any protein sequences from /data/file_1.gff. Does the file contain the assembly as well as the annotation? 2022/01/19 04:43:24 Could not extract any protein sequences from /data/file_2.gff. Does the file contain the assembly as well as the annotation? BLAST Database error: No alias or index file found for protein database [/dE1SuqpN26/output_contigs] in search path [/::]
which directory under github cloned code has the input files that can run this successfully?
Thanks. Rong
Dear Roary author and support team:
I use a RHEL 7.9 server to test Roary container. I use command 'docker pull sangerpathogens/roary' to acquire an image "docker.io/sangerpathogens/roary "
In my home directory, $ mkdir -p roary_test $ cd roary_test $ git clone https://github.com/sanger-pathogens/Roary.git -- this generate directory Roary, I moved it to 3.13 $ mv Roary 3.13 -- so $HOME/roary_test/3.13/t has a data directory I wish to use as a test.
Then, refer to README.md section "Docker - OSX/Linux/Windows/Cloud",
$ docker run --rm -it -v $HOME/roary_test/3.13/t/data/accessory_graphs:/data docker.io/sangerpathogens/roary roary -h -- this outputs the helper message
But the following command $ docker run --rm -it -v $HOME/roary_test/3.13/t/data/accessory_graphs:/data docker.io/sangerpathogens/roary roary -f . /data/*.gff returns output: Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Pubmed: 26198102
2022/01/18 23:31:25 Error: You need to provide at least 2 files to build a pan genome Usage: roary [options] *.gff Options: -p INT number of threads [1] ...... (option argument)
I am sure there are 3 gff files in the binding directory. Unfortunately, I can't get this work, I tried bind data with the upper lever data directory (which it not appears to be right from my understand), also seeing the above Error. $ ls $HOME/roary_test/3.13/t/data/accessory_graphs core_deletion file_1.fa file_2.fa file_3.fa no_accessory one_bubble two_graphs core_island file_1.gff file_2.gff file_3.gff one_branch single_gene_contig
May you please advise what I have neglected? I tried to get the docker version works, then apply singularity run on our institution research cluster. I appreciate your help.
Regards, Rong